I just moved two scenes to fragments by right-clicking on my scene and selecting move-to-fragments. The scenes disappeared from the document tree, but when I selected the Fragments tree there was nothing there. Since the scene were still open I copied them into Word just in case, then closed the project. When I reopened it they were there in Fragments, so it appears that a refresh is missing.
If the Fragments tree appeared empty when you first opened it, it probably means the tree hadn’t expanded. Double clicking on the “Fragments” title will expand the tree and should show any new fragments.