Hi B.,
I have a similar problem with my son. He's 2 1/2. For me its not the bottle problem, but the eating problem. I don't know why he won't eat, but he'll go days, even weeks without eating more than 1 bite at each meal. I keep offering foods, but nothing seems to help. I've continued giving him whole milk so he gets more fat, protein, and calories.(He's very skinny and uses LOTS of energy everyday.) He's just above the cutoff for underweight at 10%, I think. He will drink a few cups of milk everyday, but the eating part is a hit and miss. I've tried foods he likes, but that doesn't seem to change anything. I tried lots of different ways to make meals "fun", giving him goals (5 bites, then he could get down), rewards, meal replacement shakes--he wouldn't drink any of them, etc--to no avail. Our meals would usually last about 1 hour and then he started making himself throw up after taking a couple bites. I was mortified and completely frustrated! I realized that if this kept up he would be in a world of trouble and all eating activities would be a negative thing for him, which is the opposite of what I wanted. I talked to my pediatrician about it and he said, let him be. He said, when he's hungry, he'll eat. I was worried, thinking that all the effort I had been putting into getting him to eat was the only thing keeping him at the 10% and now he might lose more weight! (But I also figured if he did lose weight, maybe the Dr would then be more concerned.)
Somehow, after I stopped trying to make him he, he has started eating more on his own. Some days, no, but most days he does ok. I realized that my son did not have the stability of a routine that I think he desperately needs at this age. I'm a single mom and his dad doesn't share any of my concerns about his weight, routine, etc. In fact, it seems like he purposely messes up his routine to get back at me but it only ends up hurting my son. (That's a whole other problem) Anyway, I realized that I needed to make some drastic changes in my life in order to do the best for my son. I recently changed jobs to a more regular schedule and enrolled him into daycare. I never thought I'd want daycare, but it is really great for him.(He's only been going to daycare for the past week, but they give you daily updates on how much they eat, play, nap, etc.) He has a daily routine & schedule, meal times, play times, etc. He know what to expect, gets lots of positive reinforcement, and is eating a lot more. I don't know if you are facing any of the issues that I am, but for us the routine seemed to make the biggest difference. If you are able to structure you child's day, it might be easier to get her to eat. I basically got rid of the bottles cold turkey. Since she does drink from tippy cups, if that's all she has available to her--she will drink when she gets thirsty.
It sounds like she's got a seriously stubborn side to her and will hold out until you give in. I think its so hard not to give in when you see your child might be losing weight by not getting the bottle, but if you think about it in the long run, she will gain more weight by eating more food(instead of milk in the bottle).
I hope this helps! Let me know if you figure out something that works great. I'm always open to trying whatever I can to get more meat on my kid's bones :)