-Hope you took a Java export and a SQL Backup before you started the upgrade. if yes, try restore it in a test system and compare the settings.
-Did you check SQL Server Logs, are you getting any errors. Usually SQL upgrade is non intrusive if your SAP release support it. It should not alter the DB contents. The user permissions may get altered. If that is true, you will see alerts in the SQL error log.
- Make sure your kernel support SQL 2012.
regards
Yogesh