Are the two Forms 1096 for the same type of 1099? They can be 1099-MISC, 1099-NEC, 1099-INT or 1099-DIV. It's possible you have one 1099-MISC and the other is a 1099-NEC. The version of the form depends on the type of income you reported.
If you have not yet e-filed the Forms 1099, you can edit the forms in Quick Employer Forms (QEF) to correct the entries.
However, if the 1099's have been accepted by the IRS, you will need to use the IRS website forms and instructions for corrections. QEF does not support corrected forms at this time.
Here is the Quick Employer Forms FAQ page if you need further information.
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