I'm having a similar problem, but your solution doesn't quite get me through these challenges. I'm using TT Online.
We purchased our old primary residence in October 2017, and sold it and paid off the mortgage in September 2021. We have a single 1098 for this loan, which lists an outstanding principal of $566,074 in box 2 (i.e., the principal on Jan 1, 2021).
We purchased our new primary residence in May 2021, and have a single 1098 for this loan as well. It lists an outstanding principal of $820,000 (which was the original loan amount at purchase).
Your suggestions get me through the initial 1098 entries, I divided the box 2 amounts by the percentage of the year that I held each mortgage. But then there are additional reviews it makes me do where I need to input info that seems to conflict with the previous info I tweaked per your suggestion.
But when i go to a final review of my federal taxes, and explore the independently- calculated values for the mortgage interest deduction (which I did using the IRS worksheet), TT is still shorting my deduction by about $4000.
