that is ugly but working

while( <> ){
        while(/(E99|99)(\w+)(?=\|)|\n/){
                $key .= $`; $hash{$key}++; $key = '->'.$2;
                $_ = $';
        }
}

foreach (sort keys %hash){
        print "$_ $hash{$_}\n" if $hash{$_} >= 2;
}
[download]

run it like ./script.pl FILE1 FILE2
output will be yours repeating lines,
accordingly == 1 will show you unique lines
P.S. and turn out warnings)
P.P.S. sorry for ugliness