If understand correctly you want to flattened your folder structure? Then there is one trick:
Hide everything.
Show all hidden bodies (can be done via menu Item → Show Hidden Bodies)
Select them all (only bodies, without sketches and other items) CMD+A will help you.
Press the folder icon at the bottom of item list.
That will create one folder with all your bodies. You can select them all using shift and drag them out of the folder. Now if you want to delete all folders you have to merge the history.