It would seem simpler to say you can delete everything from the SD card and still have function of the device. The only issue is; you'll lose stuff you might want.
So.... what to do?
Make a copy of your SD card on your computer, make sure it's a good copy, and then format the SD card.
After that, you can copy the stuff back on to the SD card from the computer that you want to keep.
Done.
Your device will automatically copy directories it needs once the SD card is inserted and mounted. I have done this several times and it works without fail. Sometimes it even fixes problems I've had with software conflicts.