I have a small embedded system that supports fat32. It does not have any encryption options for the files that it saves to a external usb connected disk. Modifying the source to support encryption is not an option. Are there any external drives, or somethings that can be used to encrypted the files once the land on the disk? Something that does not require the cooperation of the embedded system?
I realize that this is a bit far fetched, but you never know!
The IronKey USB devices have on-device encryption. A Google search for encrypted hard drive yields some useful looking results.
There a few options which allow you to disarm the encryption until the next power cycle.
https://superuser.com/questions/296750/independent-hardware-based-encryption-tool-used-with-non-cooperative-system-and