I added 1099-R after taxes were accepted and pending.

[MakeMoreDave]

Is this considered an amendment and what will happen? 

[xmasbaby0]

Exactly what did you do to add the 1099R?  The only way to add it correctly would be to wait for the return to be accepted or rejected.  If it was rejected you could add the 1099R and re-file.  If the return was accepted, then you have to wait for it to be fully processed and prepare an amended return on Form 1040X to add the 1099R.   If you just went into the software while your e-file was still in "pending" the change you made went nowhere and may have messed up your return.  Remove it if you can.  

You have to amend by working from  the return exactly as it looked when originally e-filed.   

See this TurboTax support FAQ for amending a tax return - https://ttlc.intuit.com/turbotax-support/en-us/help-article/tax-return/amend-change-correct-return-a...

[JulieS]

No, if you didn't start by selecting Amend my return, you didn't do anything except change the file in TurboTax.

If you did start by selecting Amend my return and you followed the process all the way through to the end, you did amend your tax return. 

When you amend your tax return, the original and amended return are processed separately. If your original return shows a refund, you will still get that refund.

When you start your amended return, the refund goes to zero. This is based on the idea that the first return was processed and the refund was received, so now you are even with the IRS. 

If you see a refund after you complete your amended return, you will get that as a separate payment. If you see a balance due, you have to pay back that amount.