You can use the following process to transfer encrypted systems to a new EPO server:
The process discussed in those articles will use scripting. You can accomplish the same thing via the EPO web API command:
https://<EPO hostname or IP>:<EPO console port>/remote/eeadmin.enableSystemTransfer?enable=True
There are prerequisites for the system transfer to function correctly so I would recommend reading the document thoroughly before attempting the transfer.
Surely you would have a backup plan for the server being down? Why would you want to transfer all your clients to a completely different server during a server downage?
You would rebuild your existing server using the DB backup.
Machines will function as normal until they contact the server again. As hhoang says you would need to be careful about transferring encrypted clients and their recovery keys.