Look-ahead for even number of quotes:

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

say s/;(?=[^"]*(?:"[^"]*"[^"]*)*$)/&&/gr;
[download]

Output:

cd / && /path/to/R/R_latest --vanilla --args "fName='rGSDPlan';jobCode
+=682718;jo
bId=6827181;" < job682718.R > job_6827181.txt
[download]