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Sorry if this has been asked before or is a stupid question,

I have followed the BrokenThorn tutorial for writing a stage 1 bootloader but when using dd to put it on a (FAT formatted) disk it removes the FAT and the file(s) on the disk.
Shouldn't this bootloader have FAT support?

BTW, I'm on Debian Jessie if that matters

Thank you for any help and please excuse my bad English.

The very first bootloader in the Broken Thorn tutorial (Chapter 3) doesn't preserve the OEM Parameter Block, so will destroy the filesystem. The ones in Chapter 4 onwards shouldn't destroy the filesystem.

Thank you!