Update for the online version. Looks like if you delete all the forms and go in order, you can get the screens asking if the loan was paid off, so say "yes" there. The answer on original loan or refinanced later doesn't seem to matter. When you go to the CA form, you will be asked to put in the ending balances for the year. This is where you can put 0 for the original (non-refinanced) loan and any refi loan that was bought out during the year. That seems to produce a total mortgage balance that doesn't trigger the limits. I should also clarify that the Federal form forces you to put something in the "Outstanding Balance" on the main page, and I put "0" there.
Note: This only applies to the desktop version, I guess. You cannot override anything in the online version. The problem appears to be the use of the Average Balance method. If the interest rate method is used instead (divide the interest for each loan by the respective interest rate), then the average balance can be manually entered with the correct values. See: https://proconnect.intuit.com/community/help-articles/help/entering-a-refinance-in-the-excess-mortga...
