They exist as part of the CAP as it was created, so it is preserved for history. They also have huge effects on how the Pokemon plays: Persistant and Paleo Wave especially are vital for what Fidgit and Stratagem do now, but also for what the state of the game was like when they were initially released.
If there were exact matches, I would not be surprised if they were to be replaced. But GameFreak has not released copies of any of the custom moves or abilities, so they cannot be replaced. Even if they were, changing the abilities to something that didn't exist when the Pokemon were released feels off in keeping with the spirit of preserving the CAP Pokemon.
This doesn't stop us from matching changes to CAP 'mons, whether they are underwhelming or overwhelming when we get a new generation, as seen in the generation 7 CAP updates.