@herdivineshadow Yes, all permissions are lost, including notifications. Basically in the Opera Site settings, all permissions (allow/deny lists) are empty, except fow what you granted/denied within the last max 1-2 hours. And at some point (not immediately), this is also reflected in the preferences JSON file in the Opera profile directory.
So the issue is more widespread than I thought, affecting multiple (probably all) Opera browser variants on multiple (probably all) platforms. Likely it is a bug in the core code of Opera. I did not verify it another time, but IIRC the issue did not appear immediately on a fresh Opera instance, but after some days or weeks of usage. So it might have to do with the overall amount of data loaded from the profile, as if it cleared permissions as sort of a cleanup step.
