Edit/Update to answer my own question--
After a maddening wait for live chat (started at 29, twice got down to #2 in the queue before jumping back to the teens!), got things resolved.

He said that although the automated system says there will be a 3000 INR cancellation fee, it will be manually removed and the full refund will then be processed (less the 149 INR "convenience fee").

He was able to fully cancel the booking while I was on the chat. Looks like the protocol is to repeatedly ask to confirm a cancellation, he asked me 3 times to confirm that I wanted to cancel before he processed it. Now just need to wait "up to 5 days" for the refund to get back to the credit card. I took screenshots of the entire chat transcript in case there's problems later on.

Original post--

I just booked a domestic flight on Indigo for October, GWL-BDQ, connecting in DEL. It's been less than 24 hours.
I was just asked to see if I can change it to connecting in BOM instead, same day.
The fares were and are the same, whether the connection is in DEL or BOM.

I tried to modify the booking, but it looks like it's charging me a Rs2250 change fee, plus it shows only a total fare, and no credit for the fare paid. So I'm afraid I'd be double-charged if I were to proceed.

I then tried to cancel the booking altogether, figuring I'd just get a full refund (booked under 24 hours ago) and then I can rebook as desired. But when I try to cancel, it is showing a Rs 3000 cancellation fee will apply.

What do I do, just proceed with the cancellation and assume the full amount will truly be refunded to the CC? Should I call them? I'm not far from the airport, and I can even consider going there in person if that might help.

Edited to add- I tried calling, and the call dropped in mid-conversation before the agent fully got the details from me. Now am trying the live chat, am #25 in the queue.