Should I accept a bank's goodwill compensation while my RBI Ombudsman complaint is pending?

It might, so how you accept matters.

• If the offer is inadequate, decline it in writing before filing. That forecloses any argument that the matter was resolved by agreement. In one of my complaints, a ₹5,000 goodwill payment plus a card that didn't meet my request was declined by email, and the Ombudsman complaint went ahead on that basis.
• If you want the money but the problem isn't fixed, accept it as partial and without prejudice. Write something like: "I accept this payment as partial compensation, without prejudice to my complaint, which remains unresolved because [the specific issue] continues." Send it to the bank and copy the Ombudsman's case email. Otherwise the bank will report the matter as settled.
• Test any "fix" yourself before agreeing it works. Banks sometimes tell the Ombudsman an issue is fixed when it isn't. If you can show it's still broken (screenshots with dates), send that before the Ombudsman decides.
• Don't hand over account details in response to an offer you've declined. Banks sometimes ask for them to credit the amount; replying with them can be read as acceptance.

If the bank's offer becomes the basis of a closure you disagree with, see the options for non-appealable closures (a representation to the Ombudsman office, or the consumer commission).