Hello Alex_CST,
Your issue should be dated before the upgrade to the SEPM to 12.1 for sure.
For the SEP client registration work flow, it's the SEPM database information which gets the priority on everything (Domain ID, Connection Mode, Prefered Group, ...) and it's like that by design no matter if you uninstall SEP completely on the client machine and you reinstall it with a custom Client Install Settings in order to remove all previous logs, policies and force the reset of the communication settings client-server.
Here is a link for more details regarding the SEP client registration work flow => http://www.symantec.com/business/support/index?page=content&id=TECH91587
Your existing SEP clients are already known on the database to a specific PreferedGroup so as long as these information are on the SEPM Database, these SEP clients will come back to the Prefered Group already known on the database.
Is it an Embedded or SQL Database ? How many SEP clients are in this situation ?
Do you still have a SEPM Database backup from the SEP 11.X version ?
As Pete mentioned previously, the MoveClient.vbs script "might" help to resolve that, however it will probably not work with a SEPM 12.1 version (it's supposed to work correctly from 11.0 RU5 to 11.0 RU6 MP3)
MoveClients.vbs script => http://www.symantec.com/business/support/index?page=content&id=TECH157429
Please read carefully the article and recommendations provided on it before to use this tool.
Kind Regards,
A. Wesker