As the previous poster said, switch off "DisplayAlerts". But if you're doing it in perl:

use Win32::OLE;
use Win32::OLE::Const;
#...
my $ex_ol = Win32::OLE::Const->Load("Microsoft Excel 10.0 Object Libra
+ry");
my $xcl = Win32::OLE->new('Excel.Application','Quit');
#later
$xcl->Application->{DisplayAlerts}  = 0;
$doc->SaveAs($outputFileName, $$ex_ol{'xlWorkbookNormal'});
[download]

This worked fine for me on AS Perl 5.8.8 (an old build: 817). The reason you want to stop displaying alerts is that a dialog-box saying "Are you sure you want to overwrite..." comes up and stops the SaveAs from happening.

This happens even if you've made the worksheet invisible, so can lead to confusing bugs with SaveAs.