You may try this way:
before SaveAs

application.displayalerts = false
[download]

then after SaveAs restore original value:

Just to pick a nit: this is not restoring the original value. You need to query what the original value is before you start, and restore that after you are done. Make certain that you catch all exit points from your routine, or you may end up with some funky behavior.

Not being a Win32:OLE user, I don't know the required calls to do it.

--MidLifeXis

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.