It has been almost month for now ,since the release of Configmgr 2012 R2 CU4.To know more about what CU4 includes,you can refer the KB3026739 article http://support.microsoft.com/kb/3026739.
Installation of Configmgr 2014 CU4 is similar to installation of previous Cumulative updates and it is straight forward.
If you miss to install the Previous Cumulative updates,you can directly apply CU4 on Configmgr 2012 R2 .
To check if CU4 installed ,you can check the Admin console version in the About System Center Configuration Manager dialog box and version should be 5.0.7958.1501.
You can also check the registry key if CU level is updated or not .From Registry HKEY_LOCAL_MACHINE\Software\Microsoft\SMS\Setup ,CULevel should be set to 4.
After you are done with the installation of CU4,you are required to install or upgrade clients to R2 CU4 (5.0.7958.1501) version.
Before you do upgrade,you need to create collections for clients that lower the version of R2 CU4 (5.0.7958.1501).
Create collections to Upgrade Configmgr Admin Console, X86 clients and X64 clients.
R2 CU4-Console Update:
select SMS_R_System.ResourceId, SMS_R_System.ResourceType, SMS_R_System.Name, SMS_R_System.SMSUniqueIdentifier,
SMS_R_System.ResourceDomainORWorkgroup, SMS_R_System.Client from SMS_R_System inner join SMS_G_System_ADD_REMOVE_PROGRAMS on
SMS_G_System_ADD_REMOVE_PROGRAMS.ResourceID = SMS_R_System.ResourceId where
SMS_G_System_ADD_REMOVE_PROGRAMS.DisplayName = "System Center 2012 R2 Configuration Manager Console"
R2 CU4 Client X86:
select SMS_R_System.ResourceId, SMS_R_System.ResourceType, SMS_R_System.Name, SMS_R_System.SMSUniqueIdentifier,
SMS_R_System.ResourceDomainORWorkgroup, SMS_R_System.Client from SMS_R_System inner join
SMS_G_System_COMPUTER_SYSTEM on SMS_G_System_COMPUTER_SYSTEM.ResourceID = SMS_R_System.ResourceId inner join
SMS_G_System_SMS_ADVANCED_CLIENT_STATE on SMS_G_System_SMS_ADVANCED_CLIENT_STATE.ResourceID = SMS_R_System.ResourceId
where SMS_G_System_COMPUTER_SYSTEM.SystemType = "x86-based PC" and SMS_G_System_SMS_ADVANCED_CLIENT_STATE.DisplayName = "CCM Framework" and
SMS_G_System_SMS_ADVANCED_CLIENT_STATE.Version >= "5.00.7958.1000" and SMS_G_System_SMS_ADVANCED_CLIENT_STATE.Version < "5.00.7958.1501"
R2 CU4 Client X64:
select SMS_R_System.ResourceId, SMS_R_System.ResourceType, SMS_R_System.Name, SMS_R_System.SMSUniqueIdentifier,
SMS_R_System.ResourceDomainORWorkgroup, SMS_R_System.Client from SMS_R_System inner join SMS_G_System_COMPUTER_SYSTEM on
SMS_G_System_COMPUTER_SYSTEM.ResourceID = SMS_R_System.ResourceId inner join SMS_G_System_SMS_ADVANCED_CLIENT_STATE on
SMS_G_System_SMS_ADVANCED_CLIENT_STATE.ResourceID = SMS_R_System.ResourceId where SMS_G_System_COMPUTER_SYSTEM.SystemType = "x64-based PC"
and SMS_G_System_SMS_ADVANCED_CLIENT_STATE.DisplayName = "CCM Framework" and SMS_G_System_SMS_ADVANCED_CLIENT_STATE.Version >= "5.00.7958.1000"
and SMS_G_System_SMS_ADVANCED_CLIENT_STATE.Version < "5.00.7958.1501"
Deploy the respective Cumulative update to these collections and monitor the reports for client health.
Monitor the report to see if majority of your clients upgraded to current version or not using http://eskonr.com/2014/04/sccm-configmgr-2012-ssrs-reportcount-of-client-versions-2/
Note: if you wonder why did the client version version did not updated in Database,it could be because of your heartbeat discovery set to run for more number of days .Client version comes with DDR Cycle which is heartbeat discovery cycle.