Continuity in a show about a time traveler who can change history (containing other time travelers who can also change history) is naturally problematic.

We have seen a wide variety of Silurian biology and technology so it's possible that some of them experimented with cryonics, genetic manipulation and space travel around the time of the dinosaurs and periodically woke up deliberately to monitor the approach of the planetoid which would have caused disruption to other planets (like Mondas) which may have caused secondary hibernations.

The eponymous Silurians from their first story possessed a giant dinosaur like reptile, a globe depicting Pangaea and claimed to have vivisected hominids. This can only make sense if the hibernated several times.

The Silurians in The Hungry Earth return to sleep even though they don't strictly speaking have to and physically resemble the builders of the space ark.

Presumably various races of intelligent reptile (and the Mondasian humans and probably the Martians) all had different reactions to the disruption caused by the moon rolling into place.

During the RTD era planets popped in and out of the solar system with little or no effect and the moon did start to fall to Earth in one Sarah Jane Smith story but if in doubt blame the Time War.