Problem
When attempting to generate a second AFP, you get a message telling you to update Application #1 before proceeding with changes to Application #2. After updating Application #1, a new error appears asking you to undo the changes on the estimate or to refresh the AFP with the updated scheduled value.
Solution
To resolve this issue, update Application #1 and then go to the sold estimate and make edits to the line items.
Update and refresh Application #1
On the Continuation Sheet, click Update Now on the error notification to update Application #1 before starting Application #2. This takes you back to Application #1.

A confirmation message appears that says the estimate was updated after the Application for Payment was created. Click Refresh the Scheduled Value.