It will take time and patients. Make time (even if it is just a minute or two) several times a day, just to sit and talk softly to her. Every time you enter or leave the room or even pass by the door ... say hi or bye and call her by name ... this is showing her you care about her. As time/days pass open the cage door while having your little chats. If she comes to the door, praise her and give her a small piece of a treat. While checking out the treat, see if she will let you rub or scratch her gently under the chin, under the arm or on the chest ... tell her what a good girl she is. Chinchillas love attention and treats, but most of all, they love to please their humans ... be patient ... she should allow you to be friends again. Just be careful not to chase her again ... they have very long memories!
Jo Ann