Another approach (not the fastest) relying on Text::ParseWords to split the command into "words" (hopefully) like shell does:

$ perl -MText::ParseWords=quotewords -nle 'print join " ", map { $_ eq
+ ";" ? "&&" : $_ } quotewords qr/\s+/, 1, $_'
cd / ; /path/to/R/R_latest --vanilla --args "fName='rGSDPlan';jobCode=
+682718;jobId=6827181;" < job682718.R > job_6827181.txt
cd / && /path/to/R/R_latest --vanilla --args "fName='rGSDPlan';jobCode
+=682718;jobId=6827181;" < job682718.R > job_6827181.txt
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