Solved thanks to 

https://tex.stackexchange.com/questions/671439/pandoc-from-markdown-to-pdf-how-to-restart-footnote-numbering-on-each-chapter?noredirect=1#comment1668842_671439

On Tuesday, January 10, 2023 at 10:52:54 PM UTC+1 Bastien Dumont wrote:

> Pandoc, by itself, does not set the footnote numbers: in only puts 
> \footnote{} markup in the TeX file from which the PDF is generated. So you 
> have to search for how to do what you want in LaTeX (e.g. here: 
> https://tex.stackexchange.com/questions/32401/footnote-backreference-with-hyperref) 
> and to include the required commands in a custom LaTeX template or via the 
> header-includes metadata variable.
>
> Le Tuesday 10 January 2023 à 11:53:29AM, Javier Pastor a écrit :
> > I'm trying to create several chapters for an esay I'm writing, but i'd 
> like to
> > restart footnotes numbering for each chapter and I don't know how to do 
> it.
> > After searching for information, [1]I saw this on SuperUser 
> (StackExchange) and
> > I tried to replicate the solution.
> > 
> > In that example, the user tried to convert several .md files into an 
> html5 one,
> > but I'm trying to get a single PDF file. I generate the file, but it 
> doesn't
> > work as I wanted.
> > 
> > The file structure is like this:
> > 
> > chapters/
> > 01-chapter.md
> > 02-chapter.md
> > 03-chapter.md
> > format.sh
> > parse.sh
> > 
> > [2] 
> > parse.sh
> > 
> > pandoc -t pdf -o ~/Documents/test.pdf --file-scope chapters/*.md
> > 
> > 
> > format.sh
> > 
> > for f in chapters/*.md;
> > do
> > pandoc "$f" -o "$f" -t \
> > markdown+smart+footnotes-escaped_line_breaks+example_lists \
> > --columns=80;
> > done
> > 
> > In this example I have the same problem as OP had:
> > 
> > "The problem is 01-chapter.md and 02-chapter.md have both a footnote 
> [^1].
> > Basically I would like Pandoc to handle the footnotes for each file 
> separately
> > and not allow cross-referencing across my markdown files but I can't see 
> any
> > way to do this".
> > 
> > The solution, apparently, is to use the --file-scope flag. I apply it, 
> but on
> > the resulting PDF there are two problems:
> > 
> > 1. Footnote numbering doesn't restart: I had [1] and [2] in Chapter 1, 
> and [1]
> > and [2] in Chapter 2, but here I have [1] and [2] in Chapter 1 and [3] 
> and
> > [4] in Chapter 2.
> > 2. No links back from the footnotes to the text where they were used.
> > 
> > I'm just beginning to know pandoc and I don't understand exactly how that
> > works, but I guess there must be some option in pandoc that can solve 
> this. Any
> > ideas? Thank you
> > 
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> > to [3]pandoc-discus...-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org
> > To view this discussion on the web visit [4]
> https://groups.google.com/d/msgid/
> > pandoc-discuss/1e5c9c3d-21a4-4f5f-a3d7-14845a1eb300n%40googlegroups.com.
> > 
> > References:
> > 
> > [1] 
> https://superuser.com/questions/1454255/pandoc-duplicate-footnotes-multiple-files-same-name/
> > [2] https://superuser.com/posts/1454255/timeline
> > [3] mailto:pandoc-discus...-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org
> > [4] 
> https://groups.google.com/d/msgid/pandoc-discuss/1e5c9c3d-21a4-4f5f-a3d7-14845a1eb300n%40googlegroups.com?utm_medium=email&utm_source=footer
>
>

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