Apologies, but this is not correct. The CPU does not require a "charge" any more than your SD memory card does. What you're referring to is the battery-backed up RAM that was common a couple of decades ago. The settings data for the X-Pro 2 is stored in Flash memory on the main board of the camera. Fuji has already acknowledged that they are aware of some people experiencing resets and are looking into it. When they find the problem, it will be fixed via a firmware update.
The reason you have not experienced it is because you have probably not come across one of the possible sequence or scenarios that trigger the reset; not because you put in a fully charged battery.