[Alan Anderson]

When you "Run" a LabVIEW vi, or when you "Build" a project and then "Run as Startup", you automatically stop all user code already running on the cRIO. If you haven't made any uninstructed changes to the name of the compiled file, you automatically replace the previous program when you load a new one.

Unless you do something special to force them to stick around, old programs do not accumulate, so you do not need to clean them out.