Hello. This also goes to @TimAhrens: When running Kern On without re-generating kerning groups, Glyphs doesn’t register a file change once Kern On has written the new kerning. Closing the file means you lose all newly generated kerning. You need to make some other change in order to be able to save the file.
@SCarewe Thanks for the notice, @GeorgSeifert thanks for your help. I just fixed this, it will be in the next update.