IRS returned my check with interest

[DRLong31]

I filed my 2020 taxes via TT and received a refund. A few months later, I learned that a newly closed trust would not be paying its taxes as usual and I had additional income. I amended my tax form in TT and sent off the payment check. The IRS recently sent me a check equivalent to my entire payment plus interest. What happened? Should I deposit the check?

[Critter-3]

How did you send the amendment and payment ?   Did you send them together in the same envelope or did you efile the return and send the payment another way ?  

[DRLong31]

They were separate. I electronically filed the payment immediately to prevent any late payment penalties, but TT had me mail the amended return. The tracking number shows it was received. Do I need to order a tax transcript to confirm receipt?

[VolvoGirl]

Sounds like they applied the payment to your original 1040 return.   They probably hadn't even opened the amended return yet.   When you paid online did you pick the 1040X Amended return?  Maybe you picked the regular 1040.

[DRLong31]

TT used the correct form (1040X). The refund only recently processed, even though the amended form and payment were accepted in May. It is possible that the two did not connect. What are my next steps? 

[Critter-3]

First do NOT cash the check and then WAIT for them to ask for the money back when they finally process the amended return and THEN mail back the IRS check with VOID written on it.