You cannot have 5.2 and 4.6 Connection Servers in the same production cluster. The upgraded CS will upgrade the AD LDS schema and cause problems.
The only supported method for upgrading is to install a 4.6 Connection Server on Windows Server 2008 R2, decommission the old CS (ie. uninstall), then upgrade the Windows Server 2008 R2 View 4.6 CS to 5.2.
-Mike