Download “Cumulative Update 2 for ConfigMgr 2012 SP2 and ConfigMgr 2012 R2 SP1” from
https://support.microsoft.com/en-us/kb/3100144
Extract the downloaded file.
488307_ENU_x64_zip.exe
Take a backup of the SCCM server and database before upgrading.
Start the upgrade process by execution CM12_SP2R2SP1CU2-KB3100144-X64-ENU.exe
Click Yes in the UAC Windows
Click Next
Mark “I accept these license terms”
Click Next
Click Next
Click Next
Click next to update the database
Click Next to upgrade all component, SCCM Concole, and Clients
Click Next
Click Next
Click Next
Click Install
Click Next
Click Finish
And now you are ready to test the functionality of SCCM
Check the regedit to see the CU level for SCCM 2012 R2 Sp1
[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\SMS\Setup]
Console Version : 5.0.8239.1301
Version in SCCM Servicing Exension
Cloud First 
This week we’ve updated our SCCM 2012 R2 Testenvironment from CU5 to 2012 R2 SP1 CU2.
First of all we expected everything was fine, but…
When we try to update a clients SCCM agent it does not work.
Filehash in Source xml is diiferent, thats what ccmsetup.log says
What went wrong? Did we use broken or outdated sources, all downloaded from Microsoft.
Is there a chance to fix this issue and how?
Found similar issue with older Version.
https://social.technet.microsoft.com/Forums/en-US/c5b06ded-f106-44c6-898c-9410abb7a337/scepinstallexe-fails-hash-check-after-kb2828233-hotfix
Hi,
Install SCCM R2 SP1 CU2 but my console version different – 5.0.8239.1302, not 1301.
why?
Hi
Some times the console does get upgraded – it failes.
Just uninstall the console and install the Console again.
/Per