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After you file
YOU are responsible for filing your own return and making sure it was accepted for processing if you efiled or got to the correct office if you mailed it. So either the return was rejected if efiled and you did not make the correction and resubmit it timely OR you did not mail in the return or did not mail it to the correct office.
All you can do now is print, ink sign and mail in the return and attach any forms that have withholding on them. So if the 1099-R had withholding on it you will need to get a replacement from the issuing company or get an income transcript from the IRS since the TT program only keeps the info from the form but not a copy of the form itself even if you imported it. Make sure to put some kind of tracking on the envelope and then be prepared to wait for months for the paper return to process ... currently they are taking much longer than 6 months.