I did not travel on the below ticket, the train being late for more than 3 hours. I files a TDR next day.

The TDR has been rejected quoting the passenger travelled on the ticket. This is totally wrong.
I had travelled on another train the next day.

Not sure what to do or where to go.

You need to send mail to care@irctc.co.in with details of the ticket you did not travel and details of the ticket on which you travelled and then just pray to God they listen to you. Don't understand why the innocent passenger has to suffer even after paying for the tickets for the deeds of those idiot TTs who sell the ticket of the passengers illegally to others when they can cancel the current passenger who is not travelling and then officially assign the same seat to other person. Railway knows everything but not doing anything to stop this instead they like to harass the innocent passengers as they know there is no law or rules to followed in the country for government officials.