I've had the same thing happen to me in the past
This is how I do it when I get corrupted files on my FAT partition.
Don't use defrag, it is much to slow over USB.
The below will check and fix all errors on your FAT partition.
This may take about an hour.
This method uses the emergency console accessed with the B+D option.
To do a file system check on /hdd3 use below command:
If you boot with the B+D option, login as root and use
fsck.vfat -a -f -t -v -V /dev/hda3
Below is an excerpt from some instructions to get to the emergency console:
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To use the D+B option do as follows...
1. Remove power and battery from the SL-C3000.
2. Leaving the Battery Cover OFF, return the battery cover lock to the LOCKED position.
At this point examine the battery compartment.
On the edge that is closest to Zaurus Logo are a set of slots where the battery cover 'keys into' when closed.
If you look at the slot that sits almost exactly vertically central of the whole Zaurus (not the compartment),
you will notice that there is a reset button. Do NOT press it just yet.
3. Open the unit so the screen is at right angles to the base unit and sit the unit on the back of the screen so that the keyboard is accessible with one hand and the base of the unit is accessible with the other.
4. Hold down D+B on the keyboard and whilst these keys are held depress the reset button using the stylus.
5. Release the D+B keys and within a few seconds the unit should start to boot into Emergency Linux.
You can now login as root with no password (In other words, type "root" to login)
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Alternative method to get to D+B option and Also D+M option:
It makes things a LOT easier if you are already booted & running. You can simply select REBOOT from the popup menu, tap the YES box then hold down the DM or DB keys till the screen darkens & the system boots again. Can keep the Z flat & stable while using both hands to press the keys.