Yes, but they haven't paid yet!

The problem is not with amounts already paid - it's telling them that they have until October to pay any remaining amounts.

Let's say that they pay nothing with the extension on March 15th, or to be charitable,  $1000.  I record the $1000 on Screen 6.  On April 1, they discover new documents which makes their tax liability $20,000 higher. 

If they file on April 15th (in a normal year), Lacerte says that they have until October 15th to make that $19,000 payment.  That's not correct, in my opinion.