With the FBWF it should be a bit easier than with EWF to service updates on embedded devices. FBWF allows you to commit on file basis.
Since you know what your update contains (what files, directories, etc.) it is doable to implement that logic in your
DUA script.
Here is the list of Fbwfmgr commands supported:
http://msdn2.microsoft.com/en-us/library/aa940817.aspx (the command you might be looking for are addexclusion/removeexclusion).
Or, better, use FbwfCommitFile API to commit particular files (from your own app, for instance):
http://msdn2.microsoft.com/en-us/library/aa940894.aspx
The "fbwfmgr /disable" should actually work.
Btw, here is relevant article in the docs that talks about servicing Fbwf protected devices:
http://msdn2.microsoft.com/en-us/library/aa940864.aspx.
Hope this will help you.