All minor points:

Get more debug information using the special variable, $!, when checking the success of open.

Using the 3-argument form of open is also a good practice:

open my $FI, '<', 'fileExtensionList.txt or die "couldn't open input f
+ile: $!";
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It doesn't look like you use your other filehandle, $FO.

Instead of using comments for your description, you could use POD:

=head1 Description

FileExtP.pl will generate a list of files with incorrect
settings for "confirm open after download and "always show
extension"

=cut
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That way, you can get info about your program from the commandline:

$ perldoc FileExtP.pl
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