After a crash when I restart Glyphs, I get two separate Glyphs with the same file opened twice
You mean the app is opened twice?
Yes, that’s right
Maybe the system is restarting it after you started it manually?
Maybe, I am going to pay attention to what I am doing after a crash
But how is it possible to have the app and the same glyphs file opened twice?
That is not so difficult. Only when you start an app from the Finder or the Dock you will just activate the existing instance. But if you start it from the terminal, you can have one per terminal window.