Hey Madhu
those corrupted roles were in production from past 5 years
Ouch....If you have a heap of roles it might be easier to recommend a redesign and build of security. It does sound like the program must never be run again (more than like it doesn't call the BAPIs but is doing direct table updates).
I recommend you have a search through security space as your system won't be the only one in this situation.
Also, if it's taken 5 years to get to the bottom of this you can only image other build issues that are a problem
Good luck on resolving. Looks like you have a nice challenge.
Regards
Colleen