[SuperS_5]

A program that is set to run at start-up is separate from code deployed by clicking on the "run" button. The built code is loaded from Flash memory on every boot and executed immediately after booting completes. When you click the "run" arrow, it terminates and overwrites any code currently executing, with your new code. So any time you have code that you don't like, you can simply overwrite it with new and hopefully improved code. It doesn't however, do anything with your "start-up" program on the on board Flash. You can overwrite that code on the Flash memory by setting any new code to "run as start-up".

There is usually not much need to actually delete, without overwriting, the start-up code. You can disable it from running by using the dip switches on the older cRIO, or the configuration utility for the newer cRIO II. I would only use that option if mis-written is causing problems with the cRIO. Generally overwriting the start-up program is the best solution, even if that is only using the default code. (Or your last backup known to work.)