Is it possible for a TFSBuild to replace part of your web.config settings with another section?
Is this generally handled by a copy (overwrite) task on AfterBuild or AfterDropBuild where the parts of the web.config have been extracted out into their own seperate files?
UPDATE Mid '10...
If you're using Visual Studio 2010, it now comes with a new Web Config Transformation feature.
This is also a related SO Question talks about that also.