Stamp duty on DEED of confirmation

I have purchased flat in Mumbai in 2000. Sale agreement was done in May 2000 and then DEED of confirmation was done 4 month later in sept 2000.  Stamp duty was paid at old customer house

And franking of amt 26000 for stamp duty was stamp on DEED of confirmation.

Someone recently told me that this is not valid. Please guide me and tell me what is to be done here if its not correct. Entire process was done by agent  in between.

Thanks

Vikram