Sounds like you replaced the coin style batteries (CR2477) in the MPU. There is also a CR2032 battery on the back plane (right behind the MPU) that should also be replaced. Following a battery change, the NVRAM will be corrupted. That's why you get that error message. You need to do a RAM clear followed by restoring all the menu & game settings. I think there are some good YouTube videos out there on setting up the machine.
If you are going to own Bally machines, you better get used to doing some work every time you change the batteries. For the S9000 batteries last about 1-1/2 years. You will need a clear card.