I think it would be a whole lot easier to get a hash of the files in the directory. Then delete the files to be saved out of the hash? And then unlink all files in the hash? ex.

my %trash;
@trash{@file_list} = " ";
delete @trash{@saved_files};

foreach $file (keys %trash) {
    unlink $file;
}
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Tell me if I am wrong but woulnt it be a bit faster because you are not doing a conditional check in the loop?
Three