Should we submit an amended return?

[MAG19]

We submitted our 2020 tax return via efile (turbo tax) and expected a refund.  The IRS discovered there was an error with the stimulus calculation and informed us we had a balance due of $2k.  We recalculated our return and determine we should only owe the IRS $100.  We sent them a letter explaining this and also included a hard copy of the new tax return plus the $100 check payment.  The check was deposited, shortly after we received a letter demanding the original amount due of $2k.  It appears that it may have been crossed in the mail.  My question is, not wanting to confuse things more, should we e-file an amended return via Turbo tax software or should we address it by responding the payment demand letter?  Thank you    

[Critter-3]

Stop and wait ... the new notice was auto generated because the response to the first notice has not been processed yet.  

[fanfare]

"We sent them a letter explaining this and also included a hard copy of the new tax return "

This is not the correct procedure for fixing errors.

IRS will not process a second  Form 1040, revised or otherwise.

The correct process is to submit amendment on Form 1040-X.

Form 1040-X becomes your new tax return.