I think I've resolved this. By manually updating the forms.
I reviewed my federal 1098 forms from my lenders and found on the Federal Forms there was no "Date loan was paid off" and "outstanding principal" values filled in. These values are skipped in my 1098 form, but I can determine them by comparing to the other loan origination dates.
By entering the correct values in the form "Home Int Wkst" for each refinanced loan, the correct values of average loan balance are created and forwarded into the state.
TurboTax - needs to ask, if a loan is refi and paid off, but values left blank on 1098, so we can adjust these values in the step by step. We need to add payoff date and payoff balance, or
