Вам нужно использовать Workbook.SaveAs
вместо Application.Save
:
Excel.Application app = new Excel.Application();
Excel.Workbook wb = app.Workbooks.Add(missing);
...
wb.SaveAs(@"C:\temp\test.xlsx", missing, missing, missing, missing,
missing, Excel.XlSaveAsAccessMode.xlExclusive,
missing, missing, missing, missing, missing);