Emily was like that at 6 months, too. I feel for you. I vividly remember being covered in vomit several times a day, not to mention she was covered, too, and the floor, and the furniture. It got better for us - hang in there.
We never stopped PT. I recall a conversation between our dietician (who wanted t put pt on hold to conserve calories, like you said) and our pulmonologist. The pulmo's take on it was, "She's vomiting four or more times a day, anyway. THe calories will be lost regardless of wheter we stop pt or not. So, lets not let the lungs get more damaged, do pt. She encouaraged us to play aroud with the timing to see what worked. Generally, doing it during a nap was best. The pulmo did say don't worry about having her "upside down". Just on her side to do the lowers. She did vomit occasionally during pt, but she never missed a treatment. I'm glad we didn't. can't imagine how we would have "reintroduced" it once she was older and the reflux subsided.
We were on omeprozole at first. Didn't work for her. We switched to prevacid (its generic form...lanzoeprosole). We're still on it even though she rarely vomits anymore. I'm scared to stop it...and she loves it. Goes to the refrigerator and points to it, gets all excited when we get out the syringe...Crazy kid!