If you check return and look at the 990, Page1, Secc B where the check box is and CLICK (Regular left click) on that box it should take you to the area where that is created. You likely accidentally checked the box.

I covered that in my question. "There is nothing checked in the amended return input." I looked at that at least ten times. Here is a hint. The 2018 Form 990 was amended. It appears that the 2019 data file may have picked up the amended status from 2018 even though I did not check the amended return box in the 2019 input. This looks like a program error to me rather than an input issue.

Contact Support.

I tried - check the box for amended > Check return > Box is checked.

Exit client

Uncheck the box for amended > Check return > Box is checked.

You got a little bugger ghostie kinda thing hangin' in there. Support should be able to find it. 

https://proconnect.intuit.com/community/taxation/help/how-to-contact-proconnect-tax-online-for-help/...