You are always comparing the same two arrays, so your conditional can never be true. You "skip" everything.

 #...
        my @last;
        
        foreach my $key (@key)
        {
            my @submt_only = @{$hoa{$key}}[3..$#{$hoa{$key}}];

            #Check if the current array is equiv. with *one* before
            my $lc = List::Compare->new(\@last,\@submt_only);
            my $eq = $lc->is_LeqvlntR;

            if ($eq == 0 )
            {  #if they are not equivalent, assign them to a hash
                $filtered_hoa{$key} = $hoa{$key};
            }
            else
            {   #otherwise skip them
                next;
            }
            
            @last = @submt_only;
            
            
        }
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