It does matter - mostly based on what TAX ID number you used for her. You need to get her TAX ID number correct (is it her personal SS or her business EIN?).
You are supposed to transmit your 1099s to the IRS - If you already did transmit them to the IRS with her incorrect information, you have to refile the CORRECTED 1099 with the IRS for reporting purposes. Otherwise when she files her tax return her information may not match up correctly and she could be audited or charged with more income than she actually made (if they added the original 1099 to the new 1099 if it is not filed as corrected). If you have not submitted the incorrect 1099 it should not be an issue - but I would advise consulting your own CPA to make sure you are doing everything correctly.
This is not legal advice nor intended to create an attorney-client relationship. The information provided here is informational in nature only. This attorney may not be licensed in the jurisdiction which you have a question about so the answer could be only general in nature. Visit Steve Zelinger's website: http://www.stevenzelinger.com/
Mr. Zelinger has it right. The important thing is that the reporting you send to the IRS is correct, so you will have to file a corrected 1099 with IRS if your original was filed with the wrong information.