I run MR on a dedicated Windows server, I assume it will be possible to run both the unity server and the new version at the same time?
	 
	
	
Yes, you can run both servers simultaneously, as long as they're installed in different folders and use different ports 
	
	
	
	
	
		Also, will the new version have any automatic restart functionally
	 
	
	
Having a proper restart functionality is a bit problematic: You can't properly restart an application from within the application. In case of Java (the new version still needs a JVM for the plugin API), this introduces a few additional issues, since the JVM is very restrictive in this regard (once a VM, which was originally started from a certain process, is terminated, it's impossible to create a new one in the same process).
It's always safer to have an external program or script which performs the restart. However, there are a few dirty and unsupported workarounds though to still restart an application. We did some experiments with that in the past (with the Java version), but it wasn't possible to reliably restart an application (resulting in undefined behaviour - sometimes it worked, sometimes it resulted in messed up "invisible" processes, depending on the OS). This may be different in the new version, we have to run a few tests before I can give any information about that.
Windows offers a specific API to handle restarts, but that seems to be mainly intended to perform restarts after driver updates (or at least to release shared resources). I haven't looked into this API yet, but this would be obviously a very platform-specific solution (and even on Windows, this wouldn't be available on all versions).
Maybe we could alternatively implement a "soft restart", without actually performing a fresh restart of the application (not an actual restart, instead this would be more like a "reset"). I'm not sure if this is sufficient - especially if something goes wrong, there may still be unreleased resources 
In short, we will try to find a proper way to restart the server reliably, but unfortunately I can't give any guarantees 