$zip->replaceMember( 'MANIFEST.MF', $file );

##</code><code>##

$zip->replaceMember( 'META-INF/MANIFEST.MF', $file );

##</code><code>##

...
my $new_member = Archive::Zip::Member->newFromFile($file);
$zip->replaceMember( 'META-INF/MANIFEST.MF', $new_member);