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SEP 12.1 employs a side-by-side, replace on reboot installation strategy. Side-by-side means that new files are written to a new folder, referred to as a silo, isolated from the existing operational folder. Because the two versions are separated from each other, during a migration the older software is left running unchanged until the next reboot.
The primary benefit of side-by-side installation and replace on reboot is that the system continues to be protected by the existing software until the new version is in operation after the reboot.
This technique enables you to change the normal portion of the installation path during a migration, when applicable.
First upgrade SEPM to the latest version, upgrade GUP machines then SEP clients.
If clients are on the WAN network then bandwidth can be a concern. Upgrade them using other options.
Refer the following article if looking to move SEPM from one server to another.
https://www-secure.symantec.com/connect/articles/hot-move-sepm-one-server-another-server