YES!  I have had this happen in 2020 and now in 2021 software.  I spent hours on the phone with intuit and they could not figure out why it was happening.  We did every update, every error check, unchecked and re-checked boxes, sanitized the file and had intuit review it, NOTHING came up as a reason it couldn't e-file. 

The original return was e-filed by a different firm, I e-filed the amended return without issue. Then the IRS rejected (one for incorrect IP PIN and the other for Employer EIN# not matching database)  Once you open the reject notice to see what the error is, proseries no longer has the amended return available for e-file and the reason is "Federal return not complete" It obviously IS complete or it wouldn't have been able to e-file the first time when it got rejected.  The amended return doesn't even show up in the EF center anymore, just a regular federal return (even though the 1040-X is still in the file and complete).  If you scroll over in the EF center you'll see a column listing that Amended return was rejected, but no reject link to view the error notice or anything.  I ended up having to re-enter the entire return manually and then it let me e-file that new return. Of course you have to take the SSN out of the original file or it will stop you for duplicate SSN.  Really annoying to do, but its a work around that saves you from paper filing.