1.What is the use of undef here?

$pathname_versions{$1}{$2} = undef;
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2.How do I do a hash look up for the hash pathname_versions to see if $2(version in the second list) is less than the version in the list 1?

I didn't follow the discussion in the original thread, so maybe I'm missing something... but why don't you store the version as the value of the hash entries?

while (<IN>) {  # first list
    next unless ( m:(.+?)#(\d+)$: );
    $pathname_versions{$1} = $2;
}
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In this case you could later simply do (where $pathname_versions{$1} retrieves the corresponding version from the first list)

while (<IN>) {  # second list
    next unless ( m:(.+?)#(\d+)$: );
    ...
    if ( $pathname_versions{$1} < $2 ) { ...
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Actually I want the other way like below,but if i use it i am getting the below error.

        if ( $pathname_versions{$1} > $2) { #if the version in list2 i
+s less than version for the same path in list1
        print "IN\n";
        }
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Can't use string ("6") as a HASH ref while "strict refs" in use at orphan_overwrite.pl line 30, <IN> line 28