@dkh you can automatically do that in ProSeries.  Open the joint  file when they were married...and under File...scroll down to 'Split MFJ return".   I/ve done it before. Yeah the ex-spouse filed her return in April, and accepted then, etc.

So, I got live a person at Intuit, and after 1 hr and 57 minutes...and eventually getting up to a Tier 3 or Tier 4 employee, we finally got it resolved. I had 2 or 3 people at a time from Intuit sprinting all around my screen and ProSeries software.  Had to prove to each level that the xxx.sp would show up as accepted when you 'updated' xxxx_tp file.  

they never admitted what was wrong, we ended up un checking the e-file extension boxes, save the file to desktop. and delete the one in the program.  then restored it back to ProSeries and it showed accepted. Of course, we had unchecked the extension boxes...and the restored file showed late fling penalties, etc. But then I updated acks from the top toolbar (not in the EF center homebase view), and it restored the extension acceptance.

Side note, we spent the first 15 minutes with the Intuit person looking at one of my returns with the correct last 4 digits, before figuring out that was a different client.  So out of about 600 clients, I have two with the exact same last 4 digits.   Go Figure!