c:\@Work\Perl\monks>perl -wMstrict -le
"my $s = '65722417,\"1193,1\",1012,\"9,8,7\",C2,Carrier Cost Recovery 
+Fee,0.0273';
 print qq{'$s'};
 ;;
 $s =~ s{ (\" [^^\x22]+ \") }{ (my $one = $1) =~ s{,}{-}xmsg;  $one; }
+xmsge;
 print qq{'$s'};
"
'65722417,"1193,1",1012,"9,8,7",C2,Carrier Cost Recovery Fee,0.0273'
'65722417,"1193-1",1012,"9-8-7",C2,Carrier Cost Recovery Fee,0.0273'
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If you have Perl 5.14+, there is a slightly simpler version of the  s{,}{-}xmsg substitution that uses the  /r modifier. See  s/PATTERN/REPLACEMENT/msixpodualgcer in the Regexp Quote-Like Operators section of perlop.

Update: I use  [^\x22] in the char class in the  (\" [^^\x22]+ \") capture of the substitution only because my REPL doesn't like unbalanced double-quote characters! Note also that in the Windows command line, embedded double-quotes must be escaped, and that certain other characters such as ^ must be conditionally escaped. So the true version of the regex capture sub-expression is  (" [^\x22]+ ") or more simply  (" [^"]+ ") instead. Also note that this regex does not handle escaped characters within the quoted string! Also note that  tr{,}{-} (or  tr{,}{-}r with 5.14+) might be a bit quicker.