As a general technique, here's a way to emulate  [^set] where you are dealing with a potentially complex regex expression rather than a simple character class:

c:\@Work\Perl\monks>perl -wMstrict -le
"my $cd     = qr{ cd }xms;
 my $not_cd = qr{ (?! $cd) . }xms;
 ;;
 for my $s (',abcdefg,pqrstuv', ',abefg,pqrstuv', @ARGV) {
   my $t = $s;
   print qq{'$t'};
   $t =~ s{ , $not_cd* ($cd?) [^,]* , }{=$1=}xms;
   print qq{'$t' \n};
   }
"
',abcdefg,pqrstuv'
'=cd=pqrstuv'

',abefg,pqrstuv'
'==pqrstuv'
[download]

Update: Here's an example more in tune with your OPed assertion that the start and end delimiter patterns (and the optional included pattern) may be complex:

c:\@Work\Perl>perl -wMstrict -le
"my $maybe = qr{ cd? }xms;
 ;;
 my $start    = qr{ A | BC | DE?F }xms;
 my $end      = qr{ U | VW | XY?Z }xms;
 my $excluded = qr{ (?! $end | $maybe) . }xms;
 ;;
 for my $s ('AxxcdxxVWABCDEFUVWXYZ', 'BCxxxUABCDEFUVWXYZ', @ARGV) {
   my $t = $s;
   print qq{'$t'};
   $t =~ s{ $start $excluded* ($maybe?) .*? $end }{=$1=}xms;
   print qq{'$t' \n};
   }
"  BCxxcxxXZABCDEFUVWXYZ
'AxxcdxxVWABCDEFUVWXYZ'
'=cd=ABCDEFUVWXYZ'

'BCxxxUABCDEFUVWXYZ'
'==ABCDEFUVWXYZ'

'BCxxcxxXZABCDEFUVWXYZ'
'=c=ABCDEFUVWXYZ'
[download]

s/,(?:.*?(cd))?.*?,/=$1=/
[download]

Although this may be perfectly acceptable,  $1 will be undefined if it is not present in the string being searched:

c:\@Work\Perl\monks>perl -wMstrict -le
"for my $s (',abcdefg,pqrstuv', ',abefg,pqrstuv', @ARGV) {
   my $t = $s;
   print qq{'$t'};
   $t =~ s/,(?:.*?(cd))?.*?,/=$1=/;
   print qq{'$t' \n};
   }
"
',abcdefg,pqrstuv'
'=cd=pqrstuv'

',abefg,pqrstuv'
Use of uninitialized value $1 in concatenation (.) or string at -e lin
+e 1.
'==pqrstuv'
[download]

---

Give a man a fish:  <%-(-(-(-<

s/,(?:.*(cd))?.*,/$1 ? "=$1=" : "=="/e
[download]

#!/usr/bin/perl

# http://perlmonks.org/?node_id=1128703

use Data::Dump qw(pp);
use strict;
use warnings;

pp [ map 

# explanation of regex

s/
  ,      # find a comma
  .*?    # match as little as possible until you find
  (?:    # grouping for either
  (cd)     # cd  :)
  .*?      # which must be followed by as little as possible up to the
+ next
  ,        # comma
  |      # or
  ,        # a comma
  )      # end either grouping
  /      # replace with
  $1     # test for true to avoid "uninitialized" warning
  ?
  "=$1=" # =cd=
  :
  "=="   # no cd because comma was found first
  /exr   # eval, expanded, and return result of replacement(just for t
+est)

# rest of running code

  , ',abcefg,abcdefg,', ',abcdefg,abcdefg,' ];

__END__
[download]

Have you considered testing for 'cd' in the replacement?

s/,(.*?),/=@{[$1 =~ m|(cd)| && $1 ]}=/
[download]

I had not -- because I had no idea such a thing was possible. (So many Perl tricks to learn!) In fact, I still don't know how to find out more about this, because it's impossible to search Perl docs for a "@" and home in on a specific meaning. :-) What's the name of that @{ } construct?

This solves my problem perfectly, and has the bonus of not further cluttering the left-hand side of an already complex substitute pattern. Thanks for the new trick!

@{[...]} is a trick for interpolation of almost any expression into a string, explained e.g. here.

What's the name of that @{ } construct?

According to perlsecret @{[ ]} is the "baby cart" operator.

Indeed it seems you are trying to accomplish too much with a single regex! But here's another alternative:

s/(?&COMMA)(?:.*?(?:((?&CEEDEE)).*?(?&COMMA)|(?&COMMA)()))(?(DEFINE)(?
+<COMMA>,)(?<CEEDEE>cd))/=$+=/;
[download]

Just trying to see how many '?' I can get in one regex :)

s/,.*?(?:(cd).*?)??,/=$1=/
[download]

This will, of course, give "Use of uninitialized value $1 in concatenation (.)" if you use warnings. Here's a fix for that, if needed.

s;,.*?(?:(cd).*?)??,;=@{[$1 // '']}=;
[download]

or

s/,.*?(?:(cd).*?)??,/$1 ? "=$1=" : "=="/e  # without that @{[]} trick
[download]