A huge great big welcome to both you and Isabella. So glad you joined our growing family of yorkie lovers.
My ideas are often “outside the box” and may seem a bit odd, but here goes. The Rottweiler attack had to be very traumatic for both Isabella and for you and I am sure that it left some long term anxiety for both of you. Since dogs communicate primarily using their senses and are very sensitive tomates, how their human reacts, perhaps part of her fear comes from memories and/or concerns that you have about large dogs. If you feel that yorkies are “safe” playmates and large dogs aren't then it is logical that she would take cues from you.