Adding onto what @stingraze mentioned.
I recommend making sure that you always safely remove the drive before ejecting
(not saying you don't do that- I'm saying I used to do that, and it made my card corrupted. I'm very careful now!
)
Also, make sure you in the future format CF cards with the correct cluster sizes per this article:
https://www.hpcfactor.com/support/cesd/200205/maximum_supported_memory_card_file_sizes_under_windows_ce/
Quote
Maximum Cluster Size: 32KB
Here's another good guide too:
https://www.hpcfactor.com/support/cesd/200061/compact_flash_cf_cards_and_handheld_pcs/