Different script engine instances in the same R session share an accumulated class path. Furthermore, restarting a script engine does not clear the class path.

[floidgilbert]

The short answer
The only way to clear the class path is to restart the R session. This is a limitation of the rJava package that jsr223 depends on.

The explanation
The jsr223 package depends on rJava to manage low-level JVM operations. Using rJava, one R session corresponds to a single in-process JVM. Hence, all Java objects share the same class path. Currently, rJava does not provide a facility to remove entries from the class path. As a result, whenever a new script engine is instantiated with a new class path, the unique entries accumulate in the class path. The only way to clear the class path is to restart the JVM. The only way to restart the JVM is to restart the R session.