I personally just do the project files approach..
I explain more about Project Bones here:
But in simple terms, I make sure to back up the sounds and just keep the .flp (FL Studio project), as that file has everything Project Bones would give you, plus your back up. (Also making sure to remember to export Edison or Slicex files individually, too, as currently FL Studio does not save Edison or Slicex audio when using Project data files!)
So those are the two things I save!