I am having a similar problem also with the split container. The difference for me is that I am doing a copy paste and the controls disappear. The are in the designer.cs file but I cannot see them in the Design window. I have not upgraded the version of telerik as I have had it installed since the latest version was released.
I have noticed the the Designer.cs file is missing the line to add the splitPanels to their parent splitContainers.
When I manually add them in to the designer.cs file then all is well again.