Another known issue added to my list of 7 SCCM ConfigMgr 2012 R2 Known Issues. Several customers reported to Microsoft that child primary sites were entering maintenance mode after upgrading the CAS from SCCM ConfigMgr 2012 (SP1) with CU2 or CU3 to SCCM 2012 R2. I didn’t face this issue probably because I don’t use PULL DPs in my Dev environment.
As per the technet blog here, we can resolve REPLICATION ISSUE between CAS and Primary servers by re downloading the prerequisites files of SCCM 2012 R2. Microsoft had updated the prerequisite files of SCCM 2012 R2 on 14th Nov 2013. So if you’ve downloaded the prerequisite files before 14th Nov then go ahead and download it again. Especially, when you’ve PULL DPs in your environment. More details about this issue http://blogs.technet.com/b/configmgrteam/archive/2013/11/26/replication-errors-in-system-center-2012-r2-configuration-manager.aspx