Okay, yeah, it's good to do the follow-up dose, sometimes it takes a while for everything to get flushed out of their system, it is a nasty condition for them to go through because of the havoc it wreaks on their gastrointestinal tracts, then eggs get left behind, then the meds are harsh. So it can take quite a while for things to get back to normal. I would finish the follow-up dosing and then I'd still make arrangements to at least drop off a fresh fecal sample for a follow-up fecal test, that's always good practice anyway. That way you'll know if he still needs more meds, or if he's clear then you'll know he just needs some time to get his stomach settled.
Something you can try is buying a container of Soy Yogurt, all Walmarts and most grocery stores sell Silk brand Soy Yogurt with the regular yogurt. I had a lot of luck boosting appetite after a course of meds by letting their lights on first thing in the morning for an hour or so, and then giving my guy as much of the Soy Yogurt as he would eat from an eyedropper or an oral syringe, they usually really like the fruit flavors like strawberry, raspberry, blueberry, etc. The Soy Yogurt not only provides live, active cultures (acidophilus), so he's getting more probiotics, but the more important thing it does is coat their stomach which is typically upset by the combo of the bugs and the meds, so they aren't hungry. I found that about an hour or two after feeding him the Soy Yogurt he would eat close to a normal amount of live insects, just because his tummy felt better. So it's something else to try. Make sure that any Soy Yogurt you buy him is dairy-free, I know all the Silk brand Soy Yogurt is completely dairy-free...
Something else that's always a possibility is that the meds caused a secondary yeast infection in his gastrointestinal tract, now you've been giving him probiotics the entire time he was taking the meds so I doubt it's yeast, but it's always a possibility. The meds are meant to kill off everything, and unfortunately they kill off most if not all of the good, healthy, normal bacteria throughout his gastrointestinal tract, and this good, healthy, normal bacteria is what keeps yeast (and other fungi) from growing inside their guts. The probiotics are meant to replace the healthy bacteria that is killed off, but it doesn't always work that way. I've seen several beardies with some type of infection or parasite that took courses of either antibiotics, antifungals, antiparasitics, or antiprotozoans, like yours did, and then yeast was found on the follow-up fecal test. So this is yet another reason I always suggest that people get a follow-up fecal test done a day or two after the meds are completely finished. This will tell you if he still has a high coccidia count, or possibly another parasite or worm, or a secondary fungal infection, and that this is what is keeping his appetite down and he needs another round of the appropriate medication.
Hopefully he's just wiped out and his tummy is still upset from the bug and the meds, and the probiotics/soy yogurt will help settle it. Trust me, this isn't unusual at all, I know that doesn't make you feel any better about him still not eating, but I'd be willing to bet that 80% or higher of new baby beardies come to their new homes with some type of parasitic infection or worm infestation, whether they come from a pet store like Petco or PetSmart, or they cost $300-$500 from a really reputable and well-known breeder. It just happens, it's the nature of baby animals being bred and housed together. Think about puppies, they all get dewormed 3 times before going to their new homes, and if they don't they soon will be because they ALL have worms hook worms, round worms, pin worms, etc. All of them. The only difference is that dogs are mammals like us, and they have "normal" speed metabolisms and very tough gastrointestinal tracts in comparison to reptiles, who have extremely slowly metabolisms where everything happens very slowly. Plus, eating live food can be a factor as well, especially insects. But this isn't abnormal at all, unfortunately.
If you can get him to eat the slurries from an oral syringe and want him to get some protein in him, I'd suggest using an electric blender and throwing some of the dubia into the slurries. It usually entices them to eat more of the slurries because it tastes like dubia guts (yuck!), and more importantly it's much less stressful on them (and you too) than force-feeding live bugs to them. That can really take its toll on them, baby beardies become very stressed very easily, and usually force-feeding live bugs is extremely hard on them, and the person doing it. So using a blender to blend up live bugs is usually very successful, also Repashy makes an awesome product called "Repashy Grubpie" that comes in a bottle and you mix into a slurry or paste and feed to them, It's a meal-replacement for reptiles who eat mainly live insects and is made out of mostly Phoenix Worms/BSFL, so it's essentially like them eating live BSFL. So if you can find "Repashy Grubpie" at a local pet shop I'd recommend it even over the Oxbow Critical Care or Oxbow Carnivore Care that vets use, because it has a higher protein content. The Oxbow Critical Care is the second thing I'd recommend trying if you can't find the Repashy Grubpie. I know that PetSmart usually has Repashy Grubpie, though I've never seen it at any Petco. I've also seen it at an independent pet shop near me that has a huge reptile and amphibian section, so if you have any pet shops like that near you that's where I'd start.
One more alternative for you to try (take your pick on which you like) to get more protein and substance in him rather than just veggies and baby food is to buy a bottle of high-quality bearded dragon meal pellets and blend them into the baby food/veggies/Pedialyte, etc. My beardies have always had one of two specific brand bearded dragon pellets available to them in their enclosures at all times, this is more for my peace of mind than anything, so they always have access to food if they want it. So I did a ton of research about which pellets are the most nutritious and which are total junk, and most are complete garbage (never ever buy any pellets or other food that contain freeze-dried or dead bugs, like dried crickets or mealworms, they are all garbage). But there are 2 brands of pellets that are actually provide as much protein as live insects do, as well as key vitamins and minerals. The best are the RepCal Pellets, they come in a bottle of multi-colored pellets (either small, juvenile pellets, which is what I always buy, or large, adult pellets, which are better for making slurries with) that smell like fruit. They are excellent nutrition for beardies, the problem is that most beardies won't eat them. My 3 guys all pick at them, but my 5 month old boy loves them just dry. The larger adult pellets would be better for mixing into a slurry, I do this occasionally for my 1 year and 2 month old rescue boy when he has impactions. You have to soak the pellets in either baby food or Pedialyte for about 15 minutes and let them absorb the liquid, then you can either put them in a blender or just mash them with the back of a spoon and mix them into the baby food. If just for a nutritional supplement or meal replacement, I'd empty a container of baby food, whatever flavor he likes, usually butternut squash, sweet potato, or banana into a microwave-safe container and then add some of the RepCal pellets. If using the small, juvenile pellets I add 2 tablespoons full of pellets. I let them soak in the baby food for 15-20 minutes, or until they are soft and can be mashed with a spoon. Then add a little unflavored Pedialyte or water to thin it, and microwave it for 1 minute. The pellets will mix better once warmed. Then do your best to mash the pellets up really well, and you'll get a very thick slurry with some substance. They usually eat a lot of the pellet slurries, and it's essentially the same nutrition as Oxbow Critical Care. Mazuri is the other brand of pellets that are equally nutritious, but their pellets come in a bag and are little brown pellets that smell like vitamins, and my beardies won't even go near them. So the RepCal fruity pellets are by far the best available, all the other pellets available like Zilla, Flukers, etc. are complete garbage, lacking the protein content, full of sugar, etc.
So just another method of getting some protein in him. Like I said, force-feeding live insects can be very stressful on him, and can often make their appetites worse. So these are some alternatives to just feeding slurries containing baby food and veggies.