At some stage, the Sol system was given a "spring cleaning" which entailed removing most of Jupiter's moons and leaving the largest twelve. (PROSE: To the Slaughter)
Jupiter was eventually colonised by humanity. Following the achievement of independence from Earth, the colonists' government became known as the Jupiter Axis. In 2329, the Axis signed a peace agreement with Earth, ending years of tension between the two powers. In the immediate aftermath of the treaty, the surviving Jovians revealed their existence to humanity. (AUDIO: The Jupiter Conjunction)
In 2400, the Daleks invaded the solar system. Jupiter's moons were the first target. The alien inhabitants were wiped out. (Human inhabitants were not mentioned) (COMIC: Invasion of the Daleks)
In Revenge of the Cybermen, dialogue states that Jupiter had twelve moons until the arrival of Voga. As discovered later, Jupiter actually has more than sixty. Therefore, the plot of To the Slaughter explains how, further in the future, Jupiter can only have twelve moons.