If I'm following your code correctly, shouldn't the following line be using my $rulenum?

foreach my $rule ( keys %$rulelist ){
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And some formatting suggestions, particularly as your list gets longer and more nested. Perhaps change these:

   if ( defined $rulelist->{$rulenum}->{REGION} ){
      my $rule = $rulelist->{$rulenum}->{REGION};
      if ( $rule =~ s/!// ){ # handles negation
         if ( $line -> {REGIONID} == $rule ){ next RULE };
      }
      elsif ( $line -> {REGIONID} != $rule)  { next RULE };
      ...
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To this:

   if ( defined (my $rule = $rulelist->{$rulenum}->{REGION} )){
      next RULE if ( $rule =~ s/!// && $line->{REGIONID} == $rule);
      next RULE if ( $line->{REGIONID} != $rule);
      ...
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Update:Fixed a typo, I had omitted the close-paren in the first next RULE statement.