I uninstalled SQL 2012 and previous SQL 2008 R2 installations. Restarted server and installed SQL 2012 via sql4sap.vbs . After that I restored my backup and then executed SWPM MSSQL Database Upgrade but still nothing changed. ABAP is opening but Java is not. I cannot even see my Java instance in Config Tool.
To make sure I copied instance.properties file from another Solman server, adjusted IDs and server names and restarted again but still nothing.
I even resetted Secure Store passwords via Config Tool but no changes to Java situation.
Unless SAP provide a solution, my only option seems to restore whole server from a Vmware snapshot which was taken days ago and redo all of project management entries again.