If I open an .otf or .ttf font, do some edits and then save it, I will end up having a .glyphs file on disk, but the original file is gone.
Worse, if I do the same and try closing the font without saving, I am prompted to either save or revert the changes. If I choose revert, the original font file is removed, and I’m not even left with a .glyphs file.
Just tried it and I can confirm it. This is a problem that has to do with the way 10.7 and 10.8 handle files. This had been fixed but reappeared in 1.3.17 under OS 10.8.2. Until there’s a new fix, make sure you only work with copies of TTFs and OTFs.