if I change a file that is hard linked via junctions to other files with any normal editor then all the hard linked files change when doing a save. (You may need to do a refresh in your file explorer to see the changed date/size.)
If, however, I compare a (somehow random) file with a file that is hard linked to other files and save any changes to this file in CI, then the link gets broken and the changes do not propagate to its other hard linked files which makes for quite some unexpected results.
Hmm, I save file to another name first, to ensure saving is OK and do not overwrite source file before that. maybe this is a problem. I have never thought about it, thanks! I will try to fix this.
From my experience it should work if you rename the saved backup copy of the file (which I assume is in a different folder) to the actual name of the file and THEN copy the file over the file to be changed.