They may not know yet that the 1099-R has changed. It can take months for the IRS computers to scan thru all the documents submitted to them by You and the various providers. Many times, the IRS doesn't come back and complain about an "error" until almost a year later, and still can do so up to 3 years later.
So the initial tax file that the IRS "Accepted" and then processed, and issued refunds for, is just a preliminary agreement that there weren't any initially obvious conflicts in what you reported.
There is no huge hurry for you to amend to correct yoru erroneous 1099-R. Any time after you receive your refund, and then the amendment forms become available is fine. You just can't stop/bypass/interrupt what has been already filed if they "accepted" the original filing.
They generally allow up to 3 years to amend, but you should get it done in the next few months anyhow to avoid them finding the conflict first and coming after you later to explain why your original file seems to be wrong.
____________*Answers are correct to the best of my knowledge when posted, but should not be considered to be legal or official tax advice.*
