Debugged this with @ZeZaung a bit. Somehow, it was possible to re-run cloudron-setup on the existing install and this reset the database even though the app containers and data were still there. I have made a fix which should hopefully mitigate the problem.
As I said on the other thread I seem to have managed to install cloudron on Ubuntu 20.04 LTS by following your advice to use ./cloudron-setup --version 5.6.3. I've disabled automatic upgrades and I'll wait a bit to upgrade to version 6.
All is good!
Just my 2 cents here : like girish said, if you want to run other things besides cloudron, you should install cloudron in a VM.
If you really want to dedicate the whole machine to cloudron, there is really no need to bother with the additional layer of complexity, another OS to keep up to date and such. I would go bare-metal in this case. That's how I've been running cloudron for 2 years, and it's great.