it's much healthier for the dragon to just go two days without food than to have to suffer the stresses related to an unfamiliar environment. Bearded dragons are pretty good at dealing with stresses, but even though they don't show it, it still affects them. Your dragon could have trace amounts of coccidia or pinworms in him (which wouldn't necessarily be shown in a fecal examination), and the amount of stress involved in moving him around could be enough to throw his system out of balance and let the parasites get their way.
Also, dry pellets are a poor substitute for real food for a dragon. All that's really saying is 'I can't give you real food, so eat these instead'. Bearded dragons...well, reptiles in general are not designed to digest grains, and eating dry grains (pellets) will lead to a dehydrated dragon. They don't usually recognize standing water as any sort of resource because in the wild they get almost all of the moisture they need from the food they eat, and they retain moisture by hiding out in humid areas (underneath stuff, basically). In captivity they aren't usually offered a nice place to hide in humidity, but this is usually balanced by a diet that his very high in water content.
You have to really think of your reptiles as what they are. They aren't a dog or a cat, where you can leave a dish of food and a ton of water, or bring them with you. It's usually a better bet to just feed the dragon a lot beforehand, and when you come home he'll be glad to see that it's finally time to eat again. Captive bearded dragons are overfed and overweight anyways. The longest lived dragons are usually those that aren't fed everyday. There was a lady that came into this local petshop (didn't actually see her, but I heard about her a lot while conversing with the very smart staff in the reptile department). She kept her bearded dragon on a diet of greens 2-3 times a week, crickets every 2 weeks, and an occasional treat, and last I heard the dragon had reached 14 years old! I think that case is a little extreme, but people always seem to think reptiles need to eat everyday. Think about it. People feed their dragons until they are stuffed, assuming that this equals satisfaction, correct? But that's not how it works in the wild. The instincts of a dragon is to eat as much food as it can get its claws on, because in reality there is no way they will be able to get as much food as they seem to crave. We give them enough food that they are actually completely full, and then wonder why they die at 7 or 8 from kidney or liver disease (which are the leading causes of death in older dragons).
I know I've gone off on a tangent, but anyways, the healthiest dragons I've seen, are those that are not fed constantly. They grow slower, but they live longer.