Hello Brian,
Please note that replication cannot be done between two set SEPMs. Replication creates a mirror image of the Primary SEPM to the secondary, Hence in your case, the clients on one of the SEPM would not report to any SEPM.
Procedure that you could follow are :
1. Have all the clients reporting to 1 SEPM (note that the bandwidth usage would be very high if no GUPS are used)
2. Uninstall 2nd SEPM and reinstall it as a replication partner
3. Have the MSL pointing to the correct groups so that the clients reports accordingly.
Option 2.
1. Uninstall 2nd SEPM and reinstall it as a replication partner
2. Have the MSL pointing to the correct groups so that the clients reports accordingly.
3. Reconnect the clients to the 2nd SEPM
After a replication is done, the install packages need to be created only from one SEPM, for a perticular group (group A would have the clients reporting to SEPM A and Group B would have the clients reporting to SEPM B)