Natural flavor

I cut dairy almost two weeks ago and LO definitely improved with fussiness, she started decreasing the amount of times she was pooping in a day and we had one day with no blood in her diaper before it got worse again. Went to the doctor today because she has been choking on her bottle then started choking when not eating. Doctor thinks it's reflux but also wants me to give up soy. I have been eating foods with natural flavor as long as it doesn't say "contains milk". Should I give up all foods with natural flavors now or is it safe to just watch for "contains milk and soy," on the label?