I'd like to see NI develop a bullet proof way of communicating with a cRIO over TCP/IP to command that it reboot with no startup program, etc. I'm sure it can be done. The question is whether the cost to do this is warranted. I've had the cRIO lock up because of a corrupted deployment and it would not respond over the network until someone physically attended to it by setting the "no app" switch. This cRIO was mounted on a bridge over the Delaware river and was a real hassle to get to, and throw, that switch.
Suggestion: Dedicate a portion of the processor code to servicing the Ethernet ports that can't be consumed by the startup program. The user needs to always be able to reboot the cRIO and download new code.