First, I recommend becoming very familiar with this document:
https://help.inin.com/cic/mergedProjects/wh_tr/desktop/pdfs/automated_switchover_system_tr.pdf ... especially the section on switchover across a WAN.
To ship a backup server, just shut it down, ship it, and power it back on (assuming same IP/DNS). No need to disable switchover completely... though probably not a terrible idea to set to manual the first time you bring up the backup server across the VPN connection. Also keep in mind that if a lot has changed during the time the server ships that switchover may take a lot longer to start as it replicates those changes. IC may even fail to start once or twice as replication completes.
Also, the simplest change for WAN switchover is to disable the UDP ping (especially across a VPN tunnel). By default, this ping occurs every second and 5 missed pings equals a switchover event. Disabling it will cause switchover to rely on the application layer TS ping (every 10 seconds). There are other parameters that can also be set (see the doc above).
Either server can be the active server or the backup server - just depends which server is started first. So when moving the second server, switch to the remote server (the VPN will have necessary bandwidth/latency to allow CIC to operate, right?) so that it is active, shut down the server that hasn't moved, move it, and bring it back up.