I tried to set some custom shortcuts in Glyphs 3.0.3 (3091).
They’re always gone when I restart Glyphs. Not only Glyphs crashing, but also normally restarting Glyphs.
Maybe I found the reason. (?)
Glyphs crashed several times, many terminal windows are opened when Glyphs restarted every time.
I closed all terminal windows and restart Glyphs again, and now shortcuts still exist.