Deductions & credits

Apologies for so many questions on this, but it appears that when I do this, even if I refinanced late in the year (which I did), it still proportions the amount of deductible interest based on the original mortgage of my primary home, not the interest that I paid on the second home for the vast majority of the year. Is this really correct? So it's looking at my original primary home loan debt, comparing to my new debt for my primary home, and basically ignoring all the debt of my second home and assuming that's not deductible at all even though 11 of the 12 months I paid that separately before combining my loans into one. Is that really correct? Or when I do the step of filling in the boxes of 2, 3, 5, and 7, should I be putting the combination of loans from first and second homes? I'm greatly confused why refinancing two loans into one at the end of the year means the majority of the interest that I paid for the majority of the year on my second home wouldn't be deductible anymore.