I just had this last week. Here's the fix.
Check what version of the game computer rack you have. Search for NAMCO system 246. Look at the pictures to see which revision you have. I'm pretty sure you have a system 246 rev B.
If you have a 246 rev B, there is only one internal battery. To get rid of the battery02 is dead message, you need a PS1/PS2 controller and do the following:
- Take the PS1/PS2 controller and plug it in the game computer, just underneath the dongle (PS2 memory card).
- Power up the game and go into the test menu. You can use the PS1/PS2 controller to navigate the menus.
- In the test menu, select OTHERS.
- Under OTHERS, select the CDVD check. This function is not selectable without the PS1/PS2 controller connected.
- Under clock, set the date and time using the controller. Make sure you hit SET after.
- Restart the game. The message should be gone.
If you have a 246 rev A, I believe there is a second battery to replace.