Yes, use a CSV module, but if you just gotta know (I use single-quotes instead of double-quotes to keep Windoze happy):

>perl -wMstrict -le
"my $s = q{w,ww,'a,bb,ccc,3 ,ee,',4,'a,\'b,c\',d',zz};
 print qq{[$s]};
 ;;
 $s =~ s{ ( ' [^\\']* (?: \\. [^\\']*)* ' ) }
        { (my $o = $1) =~ s{,}{-}xmsg;  $o; }xmspge;
 print qq{[$s]};
"
[w,ww,'a,bb,ccc,3 ,ee,',4,'a,\'b,c\',d',zz]
[w,ww,'a-bb-ccc-3 -ee-',4,'a-\'b-c\'-d',zz]
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