Check/Voucher Included in 1099 Totals

No, the setting on the Vendor record is used solely as a default for the voucher distribution lines.  When the 1099 Work File is created, the system looks for voucher distribution lines where the "Include on 1099" option is checked.  You can, however, change the flag on the voucher distribution line by locating the voucher in Vendor Status.  Once located, right click on the voucher and choose "Change 1099 Flag".  All lines of distribution on the voucher will be listed.  Place a check mark next to those subject to 1099 reporting.