You can still use the split()/join() approach, if you utilize the LIMIT argument of split().

  my $string = "|90|93|foo|bar|91|92|95|96|906|";

  my $result = join '|',
               map { s/^9[0-6]$/X/; $_ }
               split /\|/, $string, -1;

  print $result;
  __END__
  |X|X|foo|bar|X|X|X|X|906|
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ihb