TLDR: Metabase took data from other in the same connection while database name was provided.
First of all, lesson learned about H2 databases and corruption....
After a corrupted database and problem with restoring the backups we decided to start over with MySQL database. After setting everything up and connecting to our datacenter we got a lot of errors about missing fields. We couldn't figure out why because those fields were no part of the database inserted.
After a lot of testing it seems that the MySQL connection and the provided database name were not being considered correctly and took data from other databases (in the same connection) as well.
My knowledge about how this works exactly is not enough, but maybe more people had this issue or something internally is already known?
Anyway, i hope this helps during development or someone elses problem.