After you file

Assuming this is a Federal refund, see this IRS page.  It's about a "lost" check, but the info applies to this situation, too.  They'll have to cancel that check and re-issue a new one.

It has the special IRS phone number, where you can speak to someone at the IRS or start the trace with their automated system.  You may want to speak to someone so you can get more info.

https://www.irs.gov/faqs/irs-procedures/refund-inquiries/refund-inquiries-0 

First press 1 for English.
Then press 2 for refund "lost/stolen/destroyed".

And continue following the prompts.