You should enter all income received by the S corporation on its tax return regardless of what is reported on the 1099 forms. The forms listing your old ID number can be entered as self-employment income so that they will match the forms the IRS receives. You just need to enter an expense account on your schedule C for the total of the income reported from the 1099's. That way the expense will cancel out the income. Call the expense mis-reported income or something similar.
You don't need to enter the 1099's with your old ID number into the S corporation return in TurboTax, just enter the income they report as if it wasn't reported on a 1099 form. It is doubtful you could get the issuers of the 1099's to change them, and it may cause more trouble as it could result in double-reported income, so that is probably not a good idea.
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