Frankly, I would not worry about it and assume it is all tax deductible.... here is why
while the limit is $1mm in your case, as you are refinancing 2016 debt, that $1mm is the AVERAGE for the year.
So even if we use the 'worst case' of $1,005,000 as the beginning balance, and the mortgage amortized over 10 remaining months of 2020, and assuming 4% interest for 30 years, the AVERAGE will be around $999,000 for the year.
your are under the $1million cap.
