Welcome to the Chinchilla Club Forum!
I see you are referring to both of them as "she", so I am assuming both are females.
Mystery could be seeing Cherry as a threat due to the size difference, but she may catch up to her in size eventually, but it's doubtful. Ebonies are usually smaller than standards (but not always). In the long run, the size will not matter,
unless both are naturally dominant, then there could be a problem. Mystery, the ebony, would be at a disadvantage ... eventhough I have seen some little ones be the real scrapper.
Usually, when there is just two chins, they learn to get along, but, until you know they can be left together and will snuggle instead of fight, I would not leave them alone together. Chinchillas will even act differently when their human parent is around, as apposed to when it's just the chins alone. I often set just outside the room, within hearing distance, when I let two chins be alone together for the first few times. Very smart little creatures. They like to please so that they can be the center of attention, so their actions will show this when you are in the room.
They sometimes change when you are not in the room.
Where did you get your chins? Breeder? Pet Store? Friend?
Yes, patience is a must and it is well worth it when you finally see them snuggle, share food and groom each other.
Jo Ann