Yes SEP uses a diffrent file , the file is called sylink.xml
There is no need to uninstall and reinstall the clients , just replace the sylink and the clients will move to the new SEPM.
On one machine try the following steps:
How to change a Symantec Endpoint Protection client from unmanaged to managed
1.Copy of the file Sylink.xml from the server from C:\Program Files\Symantec\Symantec Endpoint Protection Manager\data\outbox\agent\
2. On the client computer , click Start > Run, type smc -stop, and click OK.
3. Copy the Sylink.xml into the C:\Program Files\Symantec\Symantec Endpoint Protection folder, and replace any existing Sylink.xml file.
4. Click Start > Run, type smc -start, and click OK.