It might also be that 1) the motherboard has to sense a fan before starting up, and 2) the fan somehow can't tell it's rotating, I.E. the sensor has broken. Interchanging the plugs of a case fan and the water cooler/CPU fan would fool the motherboard to believe the right fan would be running. Again, this assuming the bios is set to shut down on a missing fan.
If the bios has been set to not recognize the fan due to water cooling, a failing battery or some other thing might just have reset the bios/cmos settings back to look for missing fans. Even more so after changing the battery, all settings have been reset to default including the fan settings if they were altered because of the water cooling.