Dear Srikanth,
I have faced similar issue twice and have used the same method i.e DELETE_VERSION_FROM_DB via SE24 and the issue was resolved.
Note: Please make sure that you give the correct transformation ID to the import parameter I_TRANID.
If you are still not confident enough then you always create a new TR and move it as an alternate... but I don't think even this will work as the error is linked to transformation ID not the transport.
So in your case(as you want to play safe) the best choice is to use the program given by SAP .
Best of Luck.
Regards!!