The 1098's issued are not always correct. You can change your entry of beginning/ending balances to accurately reflect your situation. You want your worksheet to be correct for the Schedule A entry, which is what the IRS sees. Keep any documentation related to changes you make from the 1098's that were issued.
You could keep your HELOC entries as reported for beginning/ending balances. For the change in servicing companies, for the first 1098 use an ending balance of $0. For the second 1098, use the correct beginning/ending balances.
Here's more info on Calculating Average Mortgage Interest (Table 1).
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