IRCTC - IRCTC repudiated EDR incorrectly

I booked a train ticket through IRCTC mobile app having following details:
PNR- **********
Name- Tarun
Train- Avadh Express (*****)
Boarding- Kanpur Central (**:**) ** Aug ****
Destination: Kota Jn(**:**) ** Aug ****
Class: *A
Ticket was booked at **:** PM on ** Aug ****, after booking ticket I received SMS from VM-IRMSa stating that train no ***** is running late by **:**hrs. So I decided to file TDR(as the chart was already prepared) and to book a different train at **:** PM on ** Aug ****.
Details of that different ticket are as under
PNR: **********
Name- Tarun
Train- SFD BDTS SF SPL (*****)
Boarding- Kanpur Govindpuri (**:**) ** Aug ****
Destination: Kota Jn(**:**) ** Aug ****
Class: *A
I travelled by this *nd train.

Now my EDR got rejected against the rules.
As the train was running late by more than *hrs and I cancelled the ticket before actual departure of train.
I must get the refund of my ticket