It'll definitely restart the Server automatically, so services will go down and come up. How quick that completes will be dependent on how many services you have and the resources on the machine. I'd imagine it copies the config-store and then restarts the Server once the config-store has been copied.
Alex, you might want to provide a little bit more information. Are you trying to move it to a new server? New folder? New Drive? Are you talking about haveing the data itself move, or are you trying to move the c:\arcgisserver directory (which I don't think you can.....it will create a new one if you wipe it out). Also, what version are you needing to do this with?
You might want to start with the help
In any case, you'll get better answers if you provide additional info.
Just trying to migrate from local storage to network storage for the arcgis directories. Which will make clustering and potential host changes easier.
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As Jon Q pointed out moving the config-store you may also look at moving the directories along with this. If in the future you ever wish to join another machine to the existing site this will only work if the config-store and directories are in a shared location that both machines can access.