There are so many people here better qualified to answer this question than I am, but I will say that switching foods a lot will cause pups to have bowel issues. Some dogs have issues with grains upsetting their tummies, some have issues with chicken (my non-yorkie dogs have issues with it), some need more protein, some less...the list can be rather endless. I would go with what you know, since your little one cannot have the green dye, and stick with the food for a while (say a few weeks), then if the pup is still having a bowel issue try mixing another food with it to get them used to the new food slowly instead of a full up switcheroo.
I wish you much luck, I know it is hard to find the right combo that makes your little one just right in the tummy area.