All my custom shortcuts disappeared after a crash using Glyphs 2 (1354). 
- They were around 15.
- System Preferences/Keyboard/Shortcuts/App Shortcuts.
- macOS Catalina 10.15.7
I restarted my computer, but they are all gone.
The shortcuts are stored in the app preferences. So if you have a backup of the preferences file, you might be able to restore them. Maybe the crash has reset them.
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Thank you Georg. 
Just to be sure, does it work if I take the com.GeorgSeifert.Glyphs2.plist from my laptop and copy it to the preferences folder on my Desktop computer? I am not sure that they are all there, but I would be able to recover most of them.
I took that file from the laptop it and I worked! 
Sorry, it is Friday and I am in a lazy mode to add all of them again by hand.