Anyone sane implementing the firmware flashing algorithm will either:
1. Just reject all IO requests from the point of the firmware update onwards. The system will see the drive disappear, but since you are using a journaling filesystem, it will be like you just pulled the power, and no data corruption will happen.
2. Complete all IO requests before the update, then update, then continue requests as before.
3. Save the firmware update, but only apply it at next powerup of the drive.