I would test it... I have a friend with several HDDs lying around that I could borrow.

I think one of the problems with writing directly to the FAT is that it's very low level, and the programming language they are using might not natively provide acces to those kinds of functions.

Another potential problem is that the file segments overlap... and since I don't know much about FAT manipulation, I don't know how difficult it would be to update it correctly minus the error checking amount.