The quickest way (AFAIK) to deploy a RT applikation (with just one reboot), is to
1. upload the new rtexe, including dependencies, to the real time target into a new folder (perhaps with the version in the name)
2. download the ni-rt.ini file from the RT target to the local disk
3. Change the RTApp.StartupApplication path to point at your newly uploaded rtexe
4. upload the edited ini-file to the RT target
5. reboot
6. new rtexe should start running
I also believe that it is possible to use private VI-server methods to edit the ini file directly on the RT target (if remote access is enabled) but I cannot check at the moment. Doing so would replace steps 2 to 4 above.
/J