I received an unexpected 1099-R after filing my 2019 return. Even though the IRS has accepted my federal return, I don't have the option to amend it. Any reason why?

[xmasbaby0]

You cannot change or add anything on the return that you just e-filed, nor can you stop it.  It is too late, just like when you put an envelope in a US mailbox on the corner.

If you left out a W-2, or a dependent, or a 1099 etc…DO NOT change your return while it is pending.  The changes will go nowhere.

Now you have to wait until the IRS either rejects or accepts your return.  If your return is rejected, you will be able to go into your account and make the necessary changes to your tax return and re-submit your return.

 If the IRS accepts your return, however, then you have to wait longer until it has been fully processed and you have received your refund.  THEN you can prepare an amended tax return and mail it in. You have to be able to work from that return exactly the way it was when it was e-filed originally.  You will need to use a form called a 1040X. You cannot e-file an amended return.  They have to be mailed, and it takes at least 2-4 months for the IRS to process an amended return.

 Meanwhile, DO NOT go in and start changing anything on your return in the system, or you will make a mess for yourself.  Sit tight and wait until you see what the IRS does with the return you just e-filed

[qharris5]

Thank you @xmasbaby0 for your reply! Like I mentioned in the original post, the IRS has already accepted my return. When you look up instructions from TurboTax on how to amend your return, it says you have to wait until it's been accepted by the IRS, which it has. But the next step in TurboTax's instructions seem to indicate that there's an "Amend" button, which there isn't. Very disheartening to hear that it takes 2-4 months for an amended return to be processed, but I guess I only have myself to blame. : (

[xmasbaby0]

The Form 1040X which you will need does not usually become available until sometime later in February.  So you have to wait to amend.  And it is better to wait until the return has been fully processed.  Sending in an amended return before the IRS even processes the original is likely to cause more confusion than you want it to.

[qharris5]

Thanks again for replying, @xmasbaby0! That makes sense and helps a lot! 

So just to make sure I understand how it'll work, I'll wait for the IRS to refund the money (and I'll actually end up having it directly deposited into my checking account). Then, after I receive the return, I'll need to submit an amended return via snail mail and wait about 4 months for it to be processed. So am I expected to not use the funds the IRS sends for those 4 months? Considering I didn't actually retain any of the funds that triggered the 1099-R (I rolled the funds from one Roth 401(k) into another), I wouldn't expect the amended return to have an impact on my refunded dollar amount. My thoughts are to simply use the refunded dollars as if I'm not amending the return.

[xmasbaby0]

What you do with your tax refund is up to you.  Just bear in mind that entering additional income can cause you to owe when you amend.