Tested on OSX. Steps to reproduce:
-create a new file in AppGameKit editor. Call it "bob.agc". Or whatever but bob works.
-write "hello" in the file in editor. do not save it. or save it if you like, who am i to say
-remove the file from the AppGameKit project in the AppGameKit editor
-edit the bob.agc file a bit more in AppGameKit editor, as it still shows in the AppGameKit editor file list but is just moved to external scope (not under project "folder")
-from outside the AppGameKit editor, delete "bob.agc". use shell, another IDE or whatever makes your day. just keep the AppGameKit editor open at the same time
-go to AppGameKit editor, double click on "bob.agc" or whatever to cause the editor to notice the file is gone
-choose to ignore and not write to disk and let the file be gone
-observe AppGameKit editor crash