even shorter and more general in usage:

  DB<229> $_=$str0
 => " bla0 \"ignore a1\" bla1 \"ignore a2\" bla2"

  DB<230> s/("[^"]*")|a/ $1 or 'A' /ge
 => 5

  DB<231> $_
 => " blA0 \"ignore a1\" blA1 \"ignore a2\" blA2"
[download]

or for the OP

  DB<226> $_=q{cd / ; /path/to/R/R_latest --vanilla --args "fName='rGS
+DPlan';jobCode=682718;jobId=6827181;" < job682718.R > job_6827181.txt
+}

  DB<227> s/("[^"]*")|;/ $1 or '&&' /ge
 => 2

  DB<228> $_
 => "cd / && /path/to/R/R_latest --vanilla --args \"fName='rGSDPlan';j
+obCode=682718;jobId=6827181;\" < job682718.R > job_6827181.txt"
[download]