The Rly proses is like this(in cace of eTicket):
Passenger not turned up on board TTE writes on his chart NT(if he dose not, Nothing much can be done)
OnLine TDR filed,
IRCTC sends TDR to railways,
both...
more... end of railway confirms passenger journey status(Destination station has the real info)
on getting confirmed reply IRCTC refunds.