According to the IRS, if you submit the return on paper after attempting to file it electronically, or if at the end of the filing season you are unable to successfully retransmit corrected returns electronically, you should attach a letter to the paper return explaining why the return was submitted on paper.
You should also include a copy of the Acknowledgment File sent by the Ogden Submission Processing Center. A copy of this ACK FILE is needed to bypass assessment of any late-filing penalties. The entire paper return should be filed at the IRS Center where the partnership would normally file their paper Form 1065 return, within ten (10) days from the date of the return that was rejected electronically.
This information applies to all years of the UltimateTax software.