They use some kind of heuristic to make change detection faster, see their documentation: http://www.cis.upenn.edu/~bcpierce/unison/download/releases/stable/uni

They use some kind of heuristic to make change detection faster, see their documentation: http://www.cis.upenn.edu/~bcpierce/unison/download/releases/stable/unison-manual.html#updates http://www.cis.upenn.edu/~bcpierce/unison/download/releases/... Maybe that's the root cause of your issues?