Whether or not it's rejected depends on what type of 1099 you entered (there are several types). If it is rejected, you can absolutely fix it and resubmit.
That said, it should be fine and be processed as long as the EIN (tax id number of the Payer) is correct. If the EIN you entered was not correct but it gets processed anyway, then the IRS may send you a notice regarding a missing 1099 form, or try to adjust your tax return. You will be able to respond with your proof of the 1099 and an explanation of what happened.
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