CORE!Frisk has been a major character in the story for quite some time.

It has been in hiding since the dawn of the new multiverse, not even Ink knows of the fact it's still alive.

They did create a new Omega timeline

Seeing as CF is omni present, they have seen everything and was aware of Peismas plan, but was in able to stop it from starting, so they then decide to ensure the safety of as many monsters as possible.

Underverse is cannon, just different to how it played out