Adding 1099-R after taxes were already pending:

[MakeMoreDave]

I got help from a turbo tax agent entering the new 1099-R, my refund went up, but the IRS and State still sent me a refund not reflecting the new higher refund.

[CatinaT1 · Accepted solution]

Your original return will still be processed as you sent it. The amended return is separate.  For future reference - don't amend a return until the original return is completely processed.

You can check the status of your amended return here.

[VolvoGirl · Accepted solution]

You will still get the refund from the first original return or still need to pay the first tax due.  In fact you should not even amend until the first return has fully processed and you get the first refund or your tax due payment has cleared.  

Then the amended return is only for the difference you get back or owe.  I think the cover sheet shows what the original return WOULD have been if you did it right the first time.

Go by the actual 1040X.  Line 18 should be your original refund amount and line 22 should be your additional refund.  If you paid on your original return it will be on line 16.  If there is an amount owed with the amendment, it will be on line 20.