Database corruption with MariaDB : Table doesn't exist in engine
Something has deleted your ibdata1 file where InnoDB keeps the dictionary. Definitely it's not MySQL who does
MariaDB crash: Table doesn't exist in engine && can't recover tables
In the end I wasn't able to recover the above server. I tried disabling one site at a time to prevent DB-access of the corrupted tables. In the end one DB contained the issue and by disabling the site mariadb didn't crash anymore.
To be sure I extracted the database data and started over on a new server. That was about 5 hours of work but after that I'm confident in my setup once again.
I've started work on restoring an old backup of the corrupted data, I've also switched back from MariaDB to Mysql as I suspect MariaDB of being the culprit.
So backups saved my day here...