Do you have a copy of the e-filed return to see EXACTLY which lines changed on the 1040 and Schedules? 

Did you do as directed and check the box in Screen 3 to apply all the new changes due to CARES? 

What happens to the bottom line if you remove that check mark.

FYI - IRS Pub 1345 would require a new signature that large a change:

"Taxpayers must sign a new declaration if the electronic return data on individual income tax returns is
changed after taxpayers signed the Declaration of Taxpayer and the amounts differ by more than either $50 to “Total income” or “AGI,” or $14 to “Total tax,” “Federal income tax withheld,” “Refund” or “Amount you owe.”

This happens occasionally when the software is updated after you've prepared the return but before you e-filed it. Obviously, some update affected the calculation of something on the return. Sometimes the software has a calculation flaw, sometimes new IRS (state) guidance comes out, and then there is the retroactive legislation our Congress had developed a habit of spewing.

My procedure is to compare the Form 8879 elements to the current software calculation prior to transmitting, particularly when there has been a long delay between the return prep and the return of the 8879.