I would just ditch all the bottles and switch to whatever cup she prefers. If there is no option to have a bottle at all she will soon adjust, it will take a few days and she will protest but stick to your guns and just offer the milk in which ever cup you choose. Your job is to offer, hers is to choose to drink or not.
I think ditching all bottles at the same time would be less confusing that keeping 1 or 2, you can talk about how she's a big girl etc, maybe let her choose a new special cup. I would let her help throw the bottles out, or the bottle fairy can take them (or Santa!) or something similar if you think she will understand so she is clear they are gone.
It won't harm her to not have milk at naps and bedtime, toddlers don't wake hungry at this age if they are eating in the day. If she is refusing milk you can up her dairy based foods, she is getting plenty more than she needs with the 3 bottles anyway.
What do you think?