I think this issue is super weird, how can a packaged installation break on an upgrade?
I guess we’ll never know.
I purged the zammad packages and reinstalled the package now it seems to work again. (without purge it didn’t work).
Putting back the storage folder and check if I need to put back anything else, but I think that isn’t necessary as all the other data should be in the database.
I thank @fliebe92 for the hints in the right direction.