Some of the machines I've worked with have had this "unmanaged" status show up with remote deployment. I found the remote deploy to be somewhat unreliable. We were'nt upgrading but rather installing a licenced version from a test deployment left behind by someone else. I still didn't want to have to re-install all the agents manually so I did the following.
Group Policy Schedule a batch uninstall script to remove all the agents from the old machines and then several minutes later run the install script to silently install from a central UNC share. It worked on almost all the machines (600+) first time and we managed to get every agent to the latest version over night. After that we ran the Product Deployment on all the machines to remove all McAfee products while still in the Lost & Found and when moving them into their designated groups on the ePO System Tree they then pulled the new licensed software and installed all the updates through the assigned client tasks.
It may seem less intuitive than the "push" method but it was way more effective than dealing with 1 out of every 5-6 machines showing up as unmanaged.
Perhaps if you explain to your boss that getting the Agent installed properly first time will save you headaches later and all the other software would be deployed automatically from that point forward.
Import the ASSC security key from the new 4.6 server into the old 4.0 server
Import the ASSC security key from the old 4.0 server into the new 4.6 server.
This step will allow the agents to talk to either server
Next try a DNS redirect on one test computer that is still connected to the 4.0 server,
Modfying the the host file adding the DNS name of the 4.0 server next to the IP address of the 4.6 server.
Open the agent monitor on this test computer and performma collect and send props - this should force it to contact the IP address of the 4.6 server.
Verify the workstation is now talking to the new 4.6 server from within the server console.
If this works, then enter a DNS CNAME alias to point all of your workstations to the new IP address and power down your old 4.0 server.
Thanks for all readings and both answers.
I asked the network administrator to help me to deploy the GPO.
When I get some results I will post here to complete the thread.