If you create a branch in TFS, you can easily merge it back later, but if you have 2 branches or folders that you want to merge, but are not related (they weren’t branched from one another) you need to do a baseless merge.

This article describes the process:

http://msdn.microsoft.com/en-us/library/bb668976.aspx

But the short end of it is that you run the following command at the VS command prompt:

tf merge /baseless c:source c:dest /recursive

It will launch the dialog box for you to manage the merge from there.