I would copy the whole structure, to be on the save side.
It are empty folders, so they don't take up any space.
Since the Genos_InstrumentInfo.n27 file of Genos 2.0 is different from firmware 1.41, you have to re-export the Genos_InstrumentInfo.n27 file from your Genos to a USB drive:
Menu -> Menu2 -> Expansion -> Export Instrument Info
Then, in YEM, delete the Genos under "Install Target" on the left. Then click the "+" to import the new Instrument Info file using the Genos_InstrumentInfo.n27 on the USB drive.
Stijn