So hundreds of years ago when Chalice was in the Calix Animi I believe that she was commanding the war against the devil and his minions, and went to confront the devil himself, and they fought with Chalice ultimately losing. Her body crumbled to ash and her head cracked and the life essence drain from the top of her head, which contained her soul, which is the little heart. When chalice was rising to heaven, she wasn't ready. she didn't want to die yet, so while she was in the astral plane, (which is right before heaven) she took out her soul, and let it float up, so she could move by her own again. This is why the legendary chalice isn't seen with a soul. You have to have a soul to get into heaven. She was able to create a portal from the astral plane to the world below her, and if she was in the normal world for too long she would melt and would never return. That's why she was stressed and was calling for help when she was in the urn. The ghosts can't hurt her, because she doesn't have her soul, which is parriable like the ghosts. if 2 parriable things touch then they both get parried, as seen in the phantom express fight. So she wasn't scared about the ghosts getting her, but rather not being able to return to the astral plane in time before she melts. The reason why Ms.Chalice looks different compared to before she died is because she goes and takes the soul and body of the host when they eat the cookie, leaving them like her, a ghost that is in the astral realm, and with the soul of the host, she turns into an alive version of her self with many characteristics of the host. Thank you for reading all of this. I thought about all of this before I fell asleep last night lmao. But these are just my headcanons, and you can have your own :)