Your step-daughter sounds like she is still feeling betrayed by you through your affair. In her world, you came into her family through devastation and left the same way. The family she had come to know after her biological mother was out of the picture included having to get used to you. Unfortunately, stepmother and stepdaughter relationships are often very fragile to begin with. When this then also came apart she is likely to have her lose trust and faith in you. This is often the case in these situations and your step-daughter’s reactions while difficult to cope with make sense.
From your description, it sounds like your stepdaughter doesn’t live with you and there are no visitation arrangements that have been made. It seems like her life is made elsewhere and her involvement with you has been minimal and agreed upon.
It also sounds like there were no efforts made at therapy between you and her after the marriage ended. Again, from your stepdaughter’s perspective you were the reminder that her mother was gone, and in you coming into the family was a constant reminder of that. Chances are she sees the affair as the cause of the end of the marriage and a reason not to trust you. Children in this situation often feel like the new family was chosen over them. Stepchildren may feel this pain even deeper. The result is that she is not likely to feel part of your life, not connected to your 3-year-old, and resentful.
If she would be willing, perhaps a meeting with you, your ex, her, and a family therapist might help. You can find qualified people in your area at the Find Help tab at the top of the page.
I wouldn’t worry much right now about what to say to your 3-year-old. Healing the relationship with your stepdaughter if it is possible must come first.