The following diagnostic is generating: Form 1040: Form 1040-X is included in this return. This return must be e-filed as an amended return. Please use E-file Amendment options in the File Return.
I figured out how to clear this! You just uncheck the e-file boxes for the 1040. The diagnostic doesn't really say what the problem is. But that is how I cleared it.
Amended returns just use a different filing option on the e-file menu. If you click on E-File in the upper bar you'll see it about halfway down in the dropdown menu.