My son needed Nutramigen because of milk protein allergy, which fortunately cleared up after he was about 12 months old. And then we had to switch him over to milk--so 2 issues may be going on here--
First, how does she handle other dairy products? Does she have any digestive problems? If so, talk with your ped. about possible milk protein allergy (which could have been the cause of the acid reflux in the first place). If not, it's not dairy allergy.
Second--the taste of milk and Nutramigen are totally different (did you ever bring yourself to try that nasty stuff? I couldn't believe he drank it!). We mixed the formula and milk together and gradually tipped the balance in favor of milk until we had eliminated the formula entirely. And we didn't only put milk in a sippy cup at first--he had the mixed formula and milk in his bottle as well as a sippy cup so it wasn't like he was only getting each in a separate cup (which can confound things if your daughter also has a preferece for the bottle over the cup).
So I guess that actually makes 3 issues--the bottle/cup issue too. Don't worry too much right now about getting rid of the bottle. My son is almost 2, he drinks out of a sippy cup, a regular cup, OR a bottle, and he enjoys his evening bottle a great deal. As long as your daughter's moving in the direction of accepting other kinds of cups besides a bottle, why pull her off of the bottle at night so quickly? Especially when you're also changing her diet (milk for formula) at the same time? Night-night is a big separation time and it's natural for children to want the comforts of babyhood at that time. As long as she's moving forward with becoming more "big girl" with sleeping and eating and socializing patterns, why push a change like this at night? I think changing just one thing at a time is often the best way to go with these ritual-bound, routine-loving wee ones.
Good luck!
K.