Mac Pro 2,1 Only Shows Flashing Question Mark After Update
A flashing question mark means it can't find system software, however, it is able to find the boot volume.  If the boot volume is on the RAID array, then it's not the RAID card.  

Try booting from installation media to see if you can see the drive.  If you can see the volume and mount it, you can recover your data.

As for the RAID battery, it keeps the last last set of write commands in the controllers memory in case there is a power failure.  I would replace it because you lose that safety net if the battery has no charge, but it's not the cause of your issue.