I wouldn't worry about it too much. From 12 months they only need about 12oz of dairy a day to get their needs met and that doesn't have to be liquid milk, all the dairy in her food counts. Milk is a drink for her now, not a food so if she doesn't drink as much it doesn't matter if you increase the dairy in her food.
I found with my DD that once I stopped the morning bottle and offered her a sippy of milk as a mid-morning snack with toast although she pretty much ignored it at first after a couple of weeks she was drinking it all. I would just stick to the cup she is most comfortable with and keep offering small amounts in that.
The issue with bottles after 1 is that it's bad for their teeth, but if they drink the milk quickly and you clean teeth after (especially at bedtime) then it really isn't a big deal if they have bottles for a while longer. I stopped the morning bottle for my two, but DS had a bedtime bottle until about 2.5 and DD until 18 months.
Laura