Apparently this difference comes from this change in font-ots.lua near line 603. If I edit the file to put back the discretionary_code argument, the output is same with new beta.

MWE (well as close to MWE I could write, requires EBGaramond unfortunately).

\language[fr]
\definefontfeature[feat][
  mode=node, ccmp=yes, calt=yes,
  liga=yes, dlig=yes, hlig=yes,
  kern=yes, mark=yes, mkmk=yes,
  onum=yes, pnum=yes, salt=yes,
  script=latn, trep=yes,
  dlig=yes, cv91=yes, ss05=no,
  protrusion=quality, expansion=quality]

\definefontfamily[mainfont][serif][EBGaramond][features=feat]
\setupbodyfont[mainfont, 9pt]

\setupalign[hanging, lesshyphenation, hz]

\starttext

\setbox\scratchbox\vbox{\hsize=8.43cm
T advint qu'il y eut famine au pays/ oultre la premiere famine/ qui fut
 au temps de Abraham. Et Izahak s'en alla vers Abimelech 
Roy des Philisthins en Gerar}\box\scratchbox

\stoptext

De : josephcanedo@gmail.com
Envoyé le :jeudi 13 octobre 2016 10:17
À : mailing list for ConTeXt users
Objet :Changes in hyphenations with 2016-10-12 beta

Dear list,

After ugrading to latest beta (to test typesetting with it for now), I noticed that some words that used to be hyphenated with previous versions are no longer hyphenated in the output, especially when the word break used to happen at a ligature (for example ‘st’ or ‘ct’).

I had a quick look to the différences in files in tex/texmf-context/tex/context/base directory and I see some changes to font handling. 

Is this expected ? Or is there any mechanism to get the old behaviour ? I’ll try to build a MWE to show this if that’s required.

Thanks a lot,

Best regards

Joseph Canedo