If they are able to process the amendment prior to them withdrawing the funds, they may just withdraw/refund the difference. However, that is unlikely. What will likely happen is that the original return will be processed completely. Then, the amended return will be processed (which can take up to 12 weeks). At that point, they would send the refund amount, if any.
That said, the amended return only shows the difference in the two amounts. For example, if you owed on the original return, the amended return should take that into consideration and only the difference would show on the Form 1040X. This is why it's best to wait until your original return as been fully processed and paid/refunded prior to filing an amended return.
--------------
GENERAL AMEND INFORMATION
Once your return has been submitted for e-file,
you cannot make any changes until it is either Accepted or Rejected. The
IRS will not receive the change. Then, when/if the
Return is accepted, you will file a new amended return. If
your return is Rejected, you can go ahead and make the change and then
resubmit the e-file.
Amending is done on
Form 1040X. Also, if your return is accepted, you should not try to
amend your return until it has been fully processed and you have received your
refund or your payment has cleared.
Amended returns have
to be printed and filed by mail. It can take the IRS up to 12 weeks or
longer to process them. If you are due a larger refund than on your
original return, your amended return should only show the difference and you
will receive a separate check for it. If you owe money on your amended
return, it will show only the new amount owed, you will have to mail a check
with the return.
How to Amend?
https://ttlc.intuit.com/replies/3288565
