Just concatenate your three fields together and use it as a hash key. The de-dup becomes a one-pass, O(1) lookup process:

my %lookup;

open IN, '<', ...
open OUT, '>', ...
while( <IN> ) {
    my( $file, $line, $rule ) = m[...(...)...(...)...(...)] 
        or warn("Bad data: '$_' line: $.\n") and next;
    if( exists $lookup{ join $;, $file, $line, $rule } ) {
        ## Duplicate, discard
        next;
    }
    else {
        ## New, record.
         $lookup{ join $;, $file, $line, $rule } = 1;
        print OUT; ## output $_
    }
}
close IN;
close OUT;
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