Yes, the DB gets modified during upgrade.
Depending on how important your data is/how much time and money you have, I would be looking at one of more of these courses of action:
1/ Roll back the upgrade.
2/ Log support case, or engage local technical resource to investigate
3/ Dig deeper into the DB yourself, look at what's going on with roles, etc. Check that system is not set to Auto-Restore.
4/ Roll back the upgrade, and try upgrade again.