Hi Venkat ,
You could certainly check with the Version management tool . ( also you could check from STMS import logs , it should be an external transport )
Your version should be 5.32 now , If you send a screenshot we will be able to confirm .
Implementing the new version (6) will do you no harm . As these are independent transports .
As for fixing the discrepency with the indexes perform ( as suggested by Venkat) as detailed in the following Note
1248769 - Inconsistency between database and ABAP Dictionary
Thanks ,
Manu