With the recently launched of the SCOM 2012 R2 UR5, one of the issue it addressed was the “Specific Case is not valid” error when you remove the agent in a server that has SQL server installed, without removing it from the SQL runas account distribution. Please refer to the previous posting here. This should save us the hassle of having to manually update the SCOM databases, without fearing that it might affect the supportability from Microsoft.
As for how to apply the patch, this is one of my favorite blog for SCOM resources
http://blogs.technet.com/b/kevinholman/archive/2015/02/22/ur5-for-scom-2012-r2-step-by-step.aspx
Information about the patch can be found here, as well as the link to download