RESOLVED.
The issue was that the upgrade gave three Views in the SQL database the wrong schema name. Support had me (actually my DBA) run a command on the SQL server to alter the schema name on the Views from "db_owner" to "dbo". This made sense since communcation was good between SEPM and the clients, but I just couldn't see them listed in the Clients view because the console couldn't open the SQL Views to present their data.
Here's a screenshot of what it looked like before the fix. Notice the first three Views have a different prefix of "db_owner" instead of "dbo".
Here's the ETrack article they sent. It was indeed the three Views they site that needed fixing.
Title
SEP clients are invisible in the SEPM console following an RU4 upgrade
Issue
SEP clients are invisible in the SEPM console following an RU4 upgrade. They continue to receive updates and show a green dot locally on the client side, but appear to be missing from all client groups in the console.
Cause
An issue during the upgrade has resulted in database views being missing or having the wrong prefix in the SEPM database.
Solution
See etrack 3378298.
The exact steps to remedy the situation will depend on if the views are missing entirely, or if they have the wrong prefix.
SQL database views can be found via the SQL Management Studio; under Databases, sem5 (the name of the SEPM database), Views.
The SQL database views affected likely are: V_SEM_COMPUTER, V_SEM_SVA_COMPUTER, V_HPP_APPLICATION_RISK
If the views are present but with a different prefix compare to the other views in the database, the following SQL script can be used:
USE database-name;
GO
ALTER SCHEMA dbo transfer incorrect_prefix.V_HPP_APPLICATION_RISK;
GO
ALTER SCHEMA dbo transfer incorrect_prefix.V_SEM_COMPUTER;
GO
ALTER SCHEMA dbo transfer incorrect_prefix.V_SEM_SVA_COMPUTER;
GO
(replace database-name and incorrect_prefix with what matches the environment)
If the views are missing entirely the etrack contains SQL scripts to recreate them.