I accidentally formatted my iriver h140 HD as NTFS in Windows (just did quick format and didn't notice NTFS was chosen as default) so I proceeded to copy music onto it. Disconnected....boot failure? huh I thought. At this point if I was using stock iriver firmware it would mean opening up the unit removing hard drive, buying a 1.8" to 3.5" adaptor, reformatting from my desktop PC, refitting the hard drive. Reconnected back to Windows.
Windows could not reformat as FAT32 so I used a Ubuntu Live cd to quick format back to FAT32. So I recovered my iriver in less than 10 minutes. :-)
So even if you don't use Rockbox, flash the bootloader as that offers more protection than stock firmware.