Alternatively, reflash the Gen3 with the "796fmt" version of the firmware reflasher. This will recreate the internal disk partion completely, and will almost certainly fix the problem. Once it is fixed, make sure that you always dismount the disk correctly before unplugging the cable.
The download URL for the full firmware reflasher is
here.
Note that this will completely "wipe" the internal memory of the Gen3, so make sure that you have a backup copy of your books, fonts, etc, before using it.