Off the bottle

My daughter is 1 1/2. At her appointment her doctor said to stop bottles cold turkey. I’m obviously not going to just stop. She only gets one at nap time and bed time. I give her milk in her supply during the day but after a couple sips she’s done with it. I’ve been told to basically do the cry it out method at nap time and she will eventually just use the sippy cup if she wants it that bad. She has breathing problems though and excessive crying makes her sick for days because everything goes to her lungs and I’m not doing that to her. She also has to have 2 scoops of oatmeal in each 8 oz bottle so she can swallow it properly. Anyone have any suggestions?