You can elect to treat the debt as not secured by the home as you describe. However, there is something entered that is causing the situation you describe. You at a minimum will get the full deduction of all the mortgage interest amounts on loans below 750,000, if used to buy, build, improve the home. Whether or not you include the 2nd mortgage the interest allocation will cover the amount entered for the primary mortgage 1098.
If some part of that mortgage was a cash out refinance and the cash was used for something other than to buy, build, or improve the home then that may change the math.
You should delete the 1098 entries and re-enter the information being sure that all the questions are answered to correctly describe the loan situation.
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