When you reboot a server in XenCenter, any virtual machines (VMs) running on it are shut down, and then the server is disconnected and rebooted. If the server is a member of a pool, the loss of connectivity on shutdown will be handled and the pool will recover when the server returns. If you shut down another pool member (not the master), the other pool members and the master will continue to function. If you shut down the master, the pool will be out of action until the master is rebooted and back on line, at which point the other members will reconnect and synchronize with the master, or until you make one of the other members into the master (which you can do via the XenServer xe command line interface (CLI)).
Note that VMs with XenServer Tools installed ("paravirtualized" VMs) will be shut down gracefully when you reboot the host server, but VMs running in HVM mode (that is, VMs without XenServer Tools installed) will be shut down using a forced shutdown; to avoid this, you should Installing XenServer Tools on all HVM virtual machines.
After a server reboot, XenCenter will attempt to reconnect to the server automatically. Once the server is reconnected, you will need to restart any VMs that were running on it unless they are configured to automatically start on host server reboot (see Change VM properties).
To reboot a server
Select the server in the Resources pane and then click Reboot on the Toolbar.