If I understand your problem correctly (my reading is: You have a list of files, you have a list of old/new filename pairs, you want to know which files have a corresponding new filename) then this problem just screams HASH.
A hash lets you index the elements by a string, so rather than searching an array (via List::Compare) for the matching element, you can write things like:
%rename_hash = ( 'oldname' => 'newname' );
if( exists $rename_hash{ $filename } ) # Does this file get changed?
{ ... }
$newname = $rename_hash{ $filename } # What's the new name?
...
You might even be able to squeeze all the code into File::Find::find()'s \&wanted parameter (though risky as you'd be changing the data File::Find is looking through).
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