There is a box on the Vendor Tab labeled 1099 Adjustment. Running the Clear 1099 Adjustment Amounts utility in the File Maintenance menu will clear any amounts from this box. This utility should be run after the 1099's have been printed for the year. If you run it before, you risk removing legitimate values associated with this year's activities.
Click File Maintenance > Accounts Payable > Clear 1099 Adjustment Amounts
Note that the 1099 box has no date associated with it. Running this utility will clear out ALL the amounts for all Vendors. If you are unsure, running the utility will display a report to indicate which Vendors have an amount in that field, so you can check them without clearing the field. When you run this utility, the Table defaults to Grantee and the Field defaults to (Vendor) 1099 Adjustment. Leave the default settings and click OK. A report will appear to show you any Vendors with an amount in that field. Once you've determined you want to clear the amounts, click Clear Values at the top and all amounts in the 1099 Adjustment field on all Grantee/Vendor records will be cleared.