You may be getting this error because you are using the SaveAs function instead of the Save function. SaveAs will prompt you like this if the file exists, Save should not. If you use the function call,
Excel_WorkbookSave (hExcelWB, NULL);
where hExcelWB is the handle to the workbook you want to save, before you close Excel. That should eliminate the prompt.
Best Regards,
Chris Matthews
National Instruments