If it's thick yellow bile, no blood in it, he's probably fine. It's usually related to hunger and can be easily solved by feeding a small snack before bedtime to hold him over. Try this first and then if it continues, you should visit your vet. You're doing the right thing by switching him over slowly. I think the big D would be more of an issue than vomiting bile so I doubt it was the bone. However, you may not want to switch both food and treats at the same time. Keep feeding the same treats as long as he doesn't have the big D until he's used to the change in food and then introduce new foods.