Board Thread:Questions and Answers/@comment-5427816-20130707071508/@comment-5627887-20130707123106

The two options in the Harvester GUI are to either shear the leaves (receiving leaf blocks in the process) or not, in which case they are destroyed as if by a player punching them, and any saplings or apples that would drop are collected by the Harvester, so the good news is you won't lose out on those BioFuel materials. As far as I know there's no option for the Harvester to completely ignore leaves, but again you don't need to wait for them to decay, the harvester will sort that out for you!