What I think can be done is just add some code to your main script. In that script it looks for an entry in the registry, or reads a .ini file for a change. Say maybe once an hour. Then IF it finds an entry of 1 for NEW CODE - it then creates a scheduled task that will run in five minutes. That scheduled task then restarts the process and resets the registry or .ini back to 0 and deletes the newly created task.

You of course externally change either the registry, ini file or some shared ini file across the network.