Can also be done as a 'pure' regex (but without need for  /e evaluation) with the Special Backtracking Control Verbs (see perlre) of 5.10+. 

>perl -wMstrict -le
"my $s =
  q{cd / ; /path/latest --van --args \"fName='foo';jobCode=12;jobId=34
+;\" < j1.R > j1.txt};
 print qq{'$s'};
 ;;
 my $d_quo = qr{ \" [^^\"]* (?: \\. [^\"]*)* \" }xms;
 ;;
 $s =~ s{ $d_quo (*SKIP)(*FAIL) | ; }{&&}xmsg;
 print qq{'$s'};
"
'cd / ; /path/latest --van --args "fName='foo';jobCode=12;jobId=34;" <
+ j1.R > j1.txt'
'cd / && /path/latest --van --args "fName='foo';jobCode=12;jobId=34;" 
+< j1.R > j1.txt'

[download]

Note: Without the escapology required by the Windoze command line, the  $d_quo regex is
    my $d_quo = qr{ " [^"]* (?: \\. [^"]*)* " }xms;
I hope that's a little more clear!

In reply to Re: In place replace, ignoring between quotes by AnomalousMonk
in thread In place replace, ignoring between quotes by Klainn

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