I’m working on a font file and after saving I get this error "The file for the document at " " has been modified by another application. Do you want to reload the version from disk? I’m clicking “Keep Glyphs Version” and it’s still reverting to the old file when I reopen it. I can tell because some of my metrics are not saving and the glyph color is changing back to an older mark.
I’m running Version 2.4 (939), on macOS Sierra 10.12.2
Do you know who is modifying the file?
I would think it’s In Design where I have my proofs. But I’m installing the OTF to test, so I’m not sure what’s causing this, since I’m working (and getting this error) in my UFO file
Did you possibly have two copies of the file open at the same time?
No 
just one file open
It might have to do with the fact that you save as UFO. I would advise to normally save as .glyphs file and only Save As .ufo if needed.
Saving as .glyphs is much faster and there are several things that can’t be stored in .ufo (hints, smart components and corners …)
I’ll try that, thanks!