Mortgage Interest deduction Issues

No. You should not override and no tax changes that affect your situation.  For the multiple 1098 entries it is usually best to start from scratch.  Delete both 1098 entries on the "Home Loan Deduction summary" page and click Done.

Next re-enter the forms 1098 as follows:

1. Primary home oldest loan
2. Primary
3. None of the above or as applicable
4. Enter form information
5. I have no points or as applicable
6. Is this the most recent 1098?  NO
7. Is this a refi or HELOC?  Neither or as applicable
8. If a refi, answer on how the funds were spent; if only spent on the home then answer "Yes"
9. Add a lender Do not click Done
10. Next, work the Primary home most recent mortgage
11. Primary
12. None of the above or as applicable
13. Enter the form information
14. Is this the most recent 1098?  YES
15. Is this a refi or HELOC?  Neither or as applicable
16. If a refi, answer on how the funds were spent; if only spent on the home then answer "Yes"
17. Add a lender Do not click Done
18. Finally, work the second home
19. Second Home
20. None of the above or as applicable
21. Enter form information
22. Yes secured by a property you own
23. I have no points or as applicable
24. Is this the most recent 1098?  Yes
25. Is this a refi or HELOC?  Neither or as applicable
26. If a refi, answer on how the funds were spent; if only spent on the home then answer "Yes"
27. Continue and Done

If this does not show the results you are expecting you should re-post here with any special circumstances such as refi's or HELOCs.