I have the same issue on 1040 returns.  Extension rejected, mailed paper copy.  Return E-filed & accepted and rejection still shows up.  Pro Series needs to add a feature to clear it as I hate seeing them on my dashboard as I use it for a check on work I still need to do and have several Filed returns with the extension rejection still showing up.  I have un-checked the E-file for extensions and it won't change the display.