You can reformat your CF cards using the Microtrack unit or by using the format utilities on the computer and this shouldn't make any difference. If you use the computer it is possible to change the format from FAT16 to FAT32 and vice-versa. This is useful as cards over 512MB should be formatted FAT32. The Microtrack unit can't change the format of the card.
It's a good idea to copy the files off of the card, reformat, and copy back what you need every once in a while as this keeps this CF card and Microtrack happy!
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