Can't remember if you can register ePO 4.0 with an ePO 4.6 server
Your easiest option is to just distribute the agent from the new server.
The only issues i can think of
- make sure you have all the management and reporting extensions checked into the new server for software that were previously managed on the old server
- make sure any special custom policies are replicated on the new server, else the clients will reset to the default polices on the new server.