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If you import into TT from QB, you're fine so long as all business income is reported. Just tell the program you don't have any 1099's and press on. Do however, keep a copy of those 1099-MISCs with your copy of the tax return, "just in case" the IRS has questions. Generally, this isn't a problem unless the IRS has reason to suspect a problem exists on your tax return.
You other option is to manually enter the 1099-MISCs into TT, and subtract the amounts reported from the "General Income" section.
Understand that when you enter a 1099-MISC into the program, that 1099-MISC itself isn't reported to the IRS. Only the total of all income reported in the Business Income section gets reported to the IRS. So I really don't see this being an issue "unless" something else on your return raises eyebrows with the IRS.
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