I did connect all the files to my original post, as well as the .docx output. When I look at my post, I can see the files there.  Do they not show up for you?

On Saturday, August 5, 2017 at 1:06:36 PM UTC-4, John MacFarlane wrote:

There's not much we can do to help without a specific sample
we can test with, including all the files needed to
reproduce the problem...

+++ Robert Goulding [Aug 04 17 12:59 ]:
>    I just compiled a fragment of an article I was writing, from markdown
>   to docx.  The command was: `pandoc -o alhazen.docx -F pandoc-citeproc
>   --bibliography=bib.bib alhazen.mmd`.
>   I received a warning about a duplicate reference. The docx file
>   contained several blank footnotes.  When I replaced the second
>   reference to `[@Alhazen1572-qk, V.9]` with an Ibid., the warning
>   disappeared, yet I *still* get empty footnotes.
>   I have used 1.19.2.1, and also a nightly beta -- with the same results.
>
>   --
>   You received this message because you are subscribed to the Google
>   Groups "pandoc-discuss" group.
>   To unsubscribe from this group and stop receiving emails from it, send
>   an email to [1]pandoc-discus...@googlegroups.com.
>   To post to this group, send email to
>   [2]pandoc-...@googlegroups.com.
>   To view this discussion on the web visit
>   [3]https://groups.google.com/d/msgid/pandoc-discuss/185cf47c-84e5-41b3-
>   8a88-ba092bc4f191%40googlegroups.com.
>   For more options, visit [4]https://groups.google.com/d/optout.
>
>References
>
>   1. mailto:pandoc-discuss+unsubscribe-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org
>   2. mailto:pandoc-...@googlegroups.com
>   3. https://groups.google.com/d/msgid/pandoc-discuss/185cf47c-84e5-41b3-8a88-ba092bc4f191@googlegroups.com?utm_medium=email&utm_source=footer
>   4. https://groups.google.com/d/optout



>% Generated by Paperpile. Check out http://paperpile.com for more information.
>% BibTeX export options can be customized via Settings -> BibTeX.
>
>@BOOK{Euclid1573-ix,
>  title    = "La prospettiva di Euclide",
>  author   = "{Euclid}",
>  editor   = "Danti, Egnazio",
>  year     =  1573,
>  address  = "Florence",
>  keywords = "Optics/Optics 3 - Renaissance;!!Cathetus;!Early Printed Books",
>  language = "it"
>}
>
>@BOOK{Euclid1557-wz,
>  title    = "Optica et Catoptrica, nunquam antehac graece aedita",
>  author   = "{Euclid}",
>  editor   = "Pena, Jean",
>  year     =  1557,
>  address  = "Paris",
>  keywords = "!!Cathetus;!Early Printed Books;Optics/Optics 3 - Renaissance",
>  language = "la"
>}
>
>@BOOK{Stevin1605-ys,
>  title    = "Mathematica hypomnemata",
>  author   = "Stevin, Simon",
>  volume   = "3: De optica",
>  year     =  1605,
>  address  = "Leiden",
>  keywords = "!Early Printed Books;Binocularism article;!!Cathetus",
>  language = "la"
>}
>
>@BOOK{Nouhuys1998-vh,
>  title     = "The age of two-faced Janus: the comets of 1577 and 1618 and the
>               decline of the Aristotelian world view in the Netherlands",
>  author    = "Nouhuys, Tabitta van",
>  publisher = "Brill",
>  series    = "Brill's studies in intellectual history",
>  year      =  1998,
>  address   = "Leiden",
>  keywords  = "
>               Aristotle--Knowledge--Astronomy;Comets--1577;Comets--1618;Astronomy--Netherlands--History;Janus
>               (Roman deity);Optics/Optics 3 - Renaissance;Renaissance Math \&
>               Science General;!!Cathetus"
>}
>
>@BOOK{Lejeune1954-ls,
>  title    = "Recherches sur la catoptrique grecque: d'apr{\`e}s les sources
>              antiques et m{\'e}di{\'e}vales",
>  author   = "Lejeune, Albert",
>  series   = "M{\'e}moires de l'Acad{\'e}mie Royale de Belgique: Classe des
>              Lettres et des Sciences Morales et Politiques",
>  year     =  1954,
>  address  = "Brussels",
>  keywords = "Optics/Optics 1 - Ancient;Optics/Refraction: Ancient and
>              Medieval;!!Cathetus",
>  language = "fr"
>}
>
>@BOOK{Kepler1951-dw,
>  title     = "Gesammelte Werke",
>  author    = "Kepler, Johannes",
>  editor    = "Caspar, Max",
>  publisher = "C. H. Beck'sche Verlagsbuchhandlung",
>  volume    = "15: Briefe 1604-1607",
>  year      =  1951,
>  address   = "Munich",
>  keywords  = "Renaissance Math \& Science General;Binocularism
>               article;!!Cathetus",
>  language  = "de"
>}
>
>@BOOK{Vimercato1565-vw,
>  title    = "In quatuor libros Aristotelis Meteorologicorum",
>  author   = "Vimercato, Francesco",
>  year     =  1565,
>  address  = "Venice",
>  keywords = "!Early Printed Books;!!Cathetus"
>}
>
>@ARTICLE{Bordiga1925-fx,
>  title    = "Giovanni Battista Benedetti: Filosofo e matematico veneziano del
>              secolo {XVI}",
>  author   = "Bordiga, Giovanni",
>  journal  = "Atti del Reale Istituto Veneto di scienze, lettere ed arti",
>  volume   =  85,
>  number   =  2,
>  pages    = "585--754",
>  year     =  1925,
>  keywords = "Optics/Optics 3 - Renaissance;Binocularism article;!!Cathetus",
>  language = "it"
>}
>
>@BOOK{Dijksterhuis1943-hn,
>  title     = "Simon Stevin",
>  author    = "Dijksterhuis, E J",
>  publisher = "Martin Nijhoff",
>  year      =  1943,
>  address   = "The Hague",
>  keywords  = "Renaissance Math \& Science General;Binocularism
>               article;!!Cathetus",
>  language  = "nl"
>}
>
>@BOOK{Stevin1605-da,
>  title    = "Wisconstighe Ghedachtenisse",
>  author   = "Stevin, Simon",
>  volume   = "3: Van de Deursichtighe",
>  year     =  1605,
>  address  = "Leiden",
>  keywords = "!Early Printed Books;Binocularism article;!!Cathetus",
>  language = "nl"
>}
>
>@BOOK{Stevin1605-pr,
>  title    = "Mathematica hypomnemata",
>  author   = "Stevin, Simon",
>  year     =  1605,
>  address  = "Leiden",
>  keywords = "!Early Printed Books;!!Cathetus",
>  language = "la"
>}
>
>@BOOK{Mersenne1623-yd,
>  title    = "Quaestiones celeberrimae in Genesim",
>  author   = "Mersenne, Marin",
>  year     =  1623,
>  address  = "Paris",
>  keywords = "!Early Printed Books;Binocularism article;!!Cathetus",
>  language = "lat"
>}
>
>@BOOK{Benedetti1585-mr,
>  title    = "Diversarum speculationum mathematicarum, et physicarum liber",
>  author   = "Benedetti, Giovanni Battista",
>  year     =  1585,
>  address  = "Turin",
>  keywords = "!Early Printed Books;Binocularism article;!!Cathetus",
>  language = "la"
>}
>
>@INCOLLECTION{Shapiro1990-rz,
>  title     = "The \textit{Optical Lectures} and the foundations of the theory
>               of optical imagery",
>  booktitle = "Before Newton: the life and times of Isaac Barrow",
>  author    = "Shapiro, Alan E",
>  editor    = "Feingold, Mordechai",
>  publisher = "Cambridge University Press",
>  pages     = "105--178",
>  year      =  1990,
>  address   = "Cambridge England ; New York",
>  keywords  = "Collections;Optics/Optics 4 - Modern;Binocularism
>               article;!!Cathetus",
>  language  = "eng"
>}
>
>@INCOLLECTION{Bellis2016-po,
>  title     = "The Perception of Spatial Depth in Kepler's and Descartes'
>               Optics: A Study of an Epistemological Reversal",
>  booktitle = "Boundaries, extents and circulations: space and spatiality in
>               early modern natural philosophy",
>  author    = "Bellis, Delphine",
>  editor    = "Vermeir, Koen and Regier, Jonathan",
>  publisher = "Springer",
>  pages     = "125--152",
>  series    = "Studies in history and philosophy of science",
>  year      =  2016,
>  address   = "Dordrecht",
>  keywords  = "Binocularism article;!!Cathetus"
>}
>
>@BOOK{Lejeune1956-in,
>  title     = "L'optique de Claude Ptol{\'e}m{\'e}e: dans la version latine
>               d'apr{\`e}s l'arabe de l'{\'e}mir Eug{\`e}ne de Sicile",
>  author    = "Lejeune, Albert",
>  publisher = "Brill",
>  year      =  1956,
>  address   = "Leiden",
>  keywords  = "Optics/Optics 1 - Ancient;Binocularism article;!!Cathetus",
>  language  = "fr"
>}
>
>@INCOLLECTION{Frangenberg1987-vk,
>  title     = "Il ``De visu'' di Giovan Battista Benedetti",
>  booktitle = "Cultura, scienze e tecniche nella Venezia del Cinquecento: atti
>               del convegno internazionale di studio Giovan Battista Benedetti
>               e il suo tempo",
>  author    = "Frangenberg, Thomas",
>  publisher = "Istituto Veneto di Scienze Lettere ed Arti",
>  pages     = "271--282",
>  year      =  1987,
>  address   = "Venice",
>  keywords  = "Optics/Optics 3 - Renaissance;Binocularism article;!!Cathetus",
>  language  = "it"
>}
>
>@ARTICLE{Omodeo2009-pe,
>  title     = "La cosmologia infinitistica di Giovanni Battista Benedetti",
>  author    = "Omodeo, Pietro Daniel",
>  journal   = "Bruniana \& Campanelliana",
>  publisher = "Accademia Editoriale",
>  volume    =  15,
>  number    =  1,
>  pages     = "181--190",
>  year      =  2009,
>  keywords  = "Renaissance Math \& Science General;Binocularism
>               article;!!Cathetus"
>}
>
>@ARTICLE{Field1985-tz,
>  title     = "Giovanni Battista Benedetti on the Mathematics of Linear
>               Perspective",
>  author    = "Field, J V",
>  journal   = "Journal of the Warburg and Courtauld Institutes",
>  publisher = "Warburg Institute",
>  volume    =  48,
>  pages     = "71--99",
>  year      =  1985,
>  keywords  = "Renaissance Math \& Science General;Optics/Optics 3 -
>               Renaissance;Binocularism article;!!Cathetus"
>}
>
>@BOOK{Lindberg1976-jm,
>  title     = "Theories of Vision from {Al-Kindi} to Kepler",
>  author    = "Lindberg, David C",
>  publisher = "University of Chicago Press",
>  year      =  1976,
>  address   = "Chicago",
>  keywords  = "Optics/Optics 5 - Surveys and General;Binocularism
>               article;!!Cathetus"
>}
>
>@BOOK{Lindberg1970-qw,
>  title     = "John Pecham and the science of optics: Perspectiva communis",
>  author    = "Lindberg, David",
>  publisher = "University of Wisconsin Press",
>  series    = "University of Wisconsin publications in medieval science",
>  year      =  1970,
>  address   = "Madison",
>  keywords  = "Optics--Early works to 1800;Optics/Optics 2 -
>               Medieval;!!Cathetus"
>}
>
>@BOOK{Smith2014-ae,
>  title     = "From Sight to Light: The Passage from Ancient to Modern Optics",
>  author    = "Smith, A Mark",
>  publisher = "University of Chicago Press",
>  year      =  2014,
>  address   = "Chicago",
>  keywords  = "Optics/Optics 5 - Surveys and General;!!Cathetus"
>}
>
>@BOOK{Darrigol2012-tj,
>  title     = "A History of Optics from Greek Antiquity to the Nineteenth
>               Century",
>  author    = "Darrigol, O",
>  publisher = "Oxford University Press",
>  year      =  2012,
>  address   = "Oxford",
>  keywords  = "Optics/Optics 5 - Surveys and General;Binocularism
>               article;!!Cathetus"
>}
>
>@PHDTHESIS{De_Wreede2007-pv,
>  title     = "Willebrord Snellius (1580-1626): a humanist reshaping the
>               mathematical sciences",
>  author    = "De Wreede, LC",
>  publisher = "igitur-archive.library.uu.nl",
>  year      =  2007,
>  school    = "Utrecht",
>  keywords  = "Optics/Optics 4 - Modern/Snell;Optics/Optics 4 -
>               Modern;!!Cathetus"
>}
>
>@ARTICLE{Gilbert1965-of,
>  title    = "Francesco Vimercato of Milan: A {Bio-Bibliography}",
>  author   = "Gilbert, Neal W",
>  journal  = "Studies in the Renaissance",
>  volume   =  12,
>  pages    = "188--217",
>  year     =  1965,
>  keywords = "Binocularism article;!!Cathetus"
>}
>
>@ARTICLE{Ruby1986-sm,
>  title    = "The Origins of Scientific ``Law''",
>  author   = "Ruby, Jane E.",
>  journal  = "Journal of the history of ideas",
>  volume   =  47,
>  number   =  3,
>  pages    = "341--359",
>  year     =  1986,
>  keywords = "Thomas Harriot;Optics/Optics 5 - Surveys and General;Law of
>              Nature;Binocularism article;!!Cathetus"
>}
>
>@ARTICLE{Dijksterhuis2004-de,
>  title    = "Once Snell Breaks Down: From Geometrical to Physical Optics in
>              the Seventeenth Century",
>  author   = "Dijksterhuis, Fokko Jan",
>  journal  = "Annals of science",
>  volume   =  61,
>  number   =  2,
>  pages    = "165--185",
>  year     =  2004,
>  keywords = "Thomas Harriot;Optics/Optics 4 - Modern;!!Cathetus"
>}
>
>@ARTICLE{Lejeune1947-xr,
>  title    = "Les lois de la r{\'e}flexion dans l'optique de Ptolem{\'e}e",
>  author   = "Lejeune, Albert",
>  journal  = "L'Antiquit{\'e} Classique",
>  volume   =  15,
>  number   =  2,
>  pages    = "241--56",
>  year     =  1947,
>  keywords = "Optics/Optics 1 - Ancient;!!Cathetus"
>}
>
>@ARTICLE{Smith1999-wc,
>  title    = "Ptolemy and the Foundations of Ancient Mathematical Optics: A
>              Source Based Guided Study",
>  author   = "Smith, A. Mark",
>  journal  = "Transactions of the American Philosophical Society",
>  volume   =  89,
>  number   =  3,
>  pages    = "1--172",
>  series   = "New Series",
>  month    =  jan,
>  year     =  1999,
>  keywords = "Optics/Optics 1 - Ancient;Binocularism article;!!Cathetus"
>}
>
>@INCOLLECTION{Lorch1985-fg,
>  title     = "{Pseudo-Euclid} on the Position of the Image in Reflection:
>               Interpretations by an Anonymous Commentator, by Pena, and by
>               Kepler",
>  booktitle = "The Light of Nature: Essays in the History and Philosophy of
>               Science presented to A. C. Crombie",
>  author    = "Lorch, Richard",
>  editor    = "North, J D and Roche, J J",
>  publisher = "Martinus Nijhoff",
>  pages     = "135--44",
>  series    = "Archives internationales d'histoire des id{\'e}es",
>  year      =  1985,
>  address   = "Dordrecht",
>  keywords  = "Optics/Optics 3 - Renaissance;!!Cathetus"
>}
>
>@ARTICLE{Turbayne1959-da,
>  title    = "Grosseteste and an Ancient Optical Principle",
>  author   = "Turbayne, Colin M.",
>  journal  = "Isis; an international review devoted to the history of science
>              and its cultural influences",
>  volume   =  50,
>  number   =  4,
>  pages    = "467--472",
>  month    =  dec,
>  year     =  1959,
>  keywords = "Optics/Optics 2 - Medieval;Binocularism article;!!Cathetus"
>}
>
>@ARTICLE{Smith2005-uz,
>  title    = "Reflections on the {Hockney-Falco} Thesis: Optical Theory and
>              Artistic Practice in the Fifteenth and Sixteenth Centuries",
>  author   = "Smith, A. Mark",
>  journal  = "Early science and medicine",
>  volume   =  10,
>  number   =  2,
>  pages    = "163--186",
>  year     =  2005,
>  keywords = "Optics/Optics 3 - Renaissance/Hockney Thesis Dupre
>              Collection;Binocularism article;!!Cathetus"
>}
>
>% The entry below contains non-ASCII chars that could not be converted
>% to a LaTeX equivalent.
>@ARTICLE{Smith2006-eg,
>  title    = "Alhacen on the Principles of Reflection: A Critical Edition, with
>              English Translation and Commentary, of Books 4 and 5 of Alhacen's
>              ``De Aspectibus'', the Medieval Latin Version of Ibn al-Haytham's
>              ``Kit{\=a}b al-Man{\=a}ẓir''. Volume One: Introduction and Latin
>              Text",
>  author   = "Smith, A. Mark",
>  journal  = "Transactions of the American Philosophical Society",
>  volume   =  96,
>  number   =  2,
>  pages    = "i--288",
>  series   = "New Series",
>  month    =  jan,
>  year     =  2006,
>  keywords = "Optics/Optics 2 - Medieval;!!Cathetus"
>}
>
>@INCOLLECTION{Chen-Morris2001-rk,
>  title     = "Kepler's Critique of the Medieval Perspectivist Tradition",
>  booktitle = "Optics and Astronomy",
>  author    = "Chen-Morris, Raz Dov and Unguru, Sabetai",
>  editor    = "Simon, G{\'e}rard and D{\'e}barbat, Suzanne",
>  publisher = "Brepols",
>  volume    =  12,
>  pages     = "83--92",
>  series    = "Proceedings of the XXth International Congress of History of
>               Science (Li{\`e}ge, 20--26 July 1997)",
>  year      =  2001,
>  address   = "Turnhout",
>  keywords  = "Optics/Optics 3 - Renaissance;Binocularism article;!!Cathetus"
>}
>
>@INCOLLECTION{Dupr2007-vk,
>  title     = "Images in the Air: Optical Games, Magic and Imagination",
>  booktitle = "Spirits Unseen: The Representation of Subtle Bodies in Early
>               Modern European Culture",
>  author    = "Dupr{\'e}, Sven",
>  editor    = "{Christine G{\"o}ttler} and {Wolfgang Neuber}",
>  publisher = "Brill",
>  volume    =  9,
>  pages     = "71--92",
>  year      =  2007,
>  address   = "Leiden; Boston",
>  keywords  = "Europe Civilization., Spirits History.;Optics/Optics 3 -
>               Renaissance;Binocularism article;!!Cathetus",
>  language  = "eng"
>}
>
>@BOOK{Euclid1895-nk,
>  title     = "Opera omnia",
>  author    = "{Euclid}",
>  editor    = "Heiberg, J L",
>  publisher = "B. G. Teubner",
>  volume    = "7: Euclidis Optica ... Catoptrica",
>  year      =  1895,
>  address   = "Leipzig"
>}
>
>@INCOLLECTION{Takahashi1992-pa,
>  title     = "The Problem of the Authorship of the Catoptrica : A Refutation
>               of the Standard View of the Work, Mainly Focussing on Heiberg's
>               Arguments",
>  booktitle = "The Medieval Latin Traditions of Euclid's Catoptrica: a critical
>               edition of De speculis with an introduction, English
>               translation, and commentary",
>  author    = "Takahashi, Ken'ichi",
>  editor    = "Takahashi, Ken'ichi",
>  publisher = "Kyushu University Press",
>  pages     = "13--37",
>  chapter   =  2,
>  year      =  1992,
>  address   = "Kyushu"
>}
>
>@BOOK{Smith1996-fg,
>  title     = "Ptolemy's Theory of Visual Perception: An English Translation of
>               the ``Optics'' with Introduction and Commentary",
>  author    = "Smith, A Mark",
>  publisher = "American Philosophical Society",
>  series    = "Transactions of the American Philosophical Society",
>  year      =  1996,
>  address   = "Philadelphia"
>}
>
>@BOOK{Weinrich1998-zr,
>  title     = "Die Lichtbrechung in den Theorien von Descartes und Fermat",
>  author    = "Weinrich, Klaus",
>  publisher = "F. Steiner",
>  series    = "Sudhoffs Archiv: Beihefte",
>  year      =  1998,
>  address   = "Stuttgart",
>  language  = "de"
>}
>
>
>@BOOK{Alhazen1572-qk,
>  title    = "Opticae thesaurus",
>  author   = "{Alhazen} and {Witelo}",
>  editor   = "Risner, Friedrich",
>  year     =  1572,
>  address  = "Basel",
>  language = "la"
>}
>
>@ARTICLE{De_Waard1935-fj,
>  title     = "Le manuscrit perdu de Snellius sur la r{\'e}fraction",
>  author    = "De Waard, Cornelis",
>  journal   = "Janus",
>  publisher = "Brill",
>  volume    =  39,
>  pages     = "51--73",
>  year      =  1935,
>  language  = "fr"
>}