I amended an accepted return and the IRS cash both checks. How do I get a refund for the difference?

You have two (2) options:

1. You can amend your return again and enter amount paid with return, Form 1040X Line 16, Total amount paid with request for extension of time to file, tax paid with original return, and additional tax paid after return was filed.
2. Another option is to wait for the IRS to process your returns. They will generally catch the overpayment, send you an explanation letter and you'll be able to request the refund.

 

Thanks Helen. How long does it usually take before they catch the mistake?

It depends.

 

The IRS is still in the process of catching up on paper returns as well as processing returns for 2020 with all of the tax season changes.

 

I'd recommend checking the following websites to see updates to your account.  Typically, it takes approximately 16 weeks for them to process an amended return.

 

Where's my amended return information from the IRS

 

View your tax account with the IRS