You *could* do it in three steps:

my $string = "AAbfwercB(A)fjklASZaB(A)xvASABAB(A)gfdaZAA";
my @chunks = split(/B\(A\)/, $_);
$_ =~ tr/A/Z/ foreach @chunks;
$string = join 'B(A)', @chunks;
[download]

My guess is that it's a little slow, though. I'd reverse $string first, myself.