Thank you @nebulon for solving this issue off-forums. For future reference: problem was caused by the external storage being unmounted after a reboot. Remounting the storage drive (I use a netcup VPS) and then repairing in the Cloudron dashboard solved the problem. Including the mounting in /etc/fstab solved this issue for following updates/reboots.

Thanks @fbartels @nebulon @murgero I am going to take a look at Hetzner storage boxes. It limits me to 10 TB max. In future if you guys can add quota system per user or app. That would be great.

This was resolved offline - most issues where related to unbound (the internal DNS server) being down. Fixed by System -> restart unbound.

@doomilation Yes, what you have done should work. You don't have to move out appsdata and platformdata.

@nebulon Okay. Thanks for clarification!