If you mean, one SQL DB is connected 3 SEPM servers(just to clarify, this is not replication), just turn off the the SEPM services on all the 3 SEPM servers before upgrading the SEPM. After the upgrade is complete on one server, the other 2 SEPM won't be able to connect to DB until you upgrade them as well.
If you mean that 3 SEPM servers (with their own individual databases) are configured to replicate (whcih syncs the data on all 3 databases), then you will need to delete thje replication partner on all the SEPM servers before the upgrade. Once the upgrade is complete, the replication partners need to be added again.