Open two documents, one with branches. Copy the contents with branches into the other document. Notice that the branch-boxes are created, but document->settings shows no branches at all.
This at least causes the problem that one cannot turn branches on and off, and possibly other internal problems. (Can LyX save that document in a sane manner?) Creating the missing branches manually works, the pasted branches can then be turned on and off as usual. Helge Hafting