Flashing firmware is always risky. If the drive is responding and if there is a dos version of the flash, unplug the hard drives and flash from the floppy drive only. If the flash is only windows based, run the flash in safe mode.

There is a disclaimer on most firmware upgrades, you toast it, it's your problem. Have you tried reading the data on the drive in dos? Will the dvd boot the win98 cd for you?