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If the total of the original group of 1099 forms that you sent in matched the total on the 1096 summary form that you sent in, then you do not need to resubmit the entire batch of forms.
If all you did was fail to include one 1099 form in your reporting, then simply file that one form with a new 1096 form and send those forms only to the IRS. There is no need to resubmit the entire group again. You would just submit the one 1099 form that you failed to include with the first batch and then on the 1096 form just show the total for that one form.
Refer to the following 1099 instructions. In particular, look at page 5 at the very bottom, the paragraph headed "Multiple Filings".
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