The drug your vet is using seems to be the main medication used to treat entamoeba from what i learned with a bit of research.
During the treatment have you been following strict quarentee and sterization procedures? (ie keep dragon in as simple a cage as possible, clean daily, throw out substrate (it should be something easy like papertowel), clean and disinfect everything that goes in or comes out of your dragon's cage, including your hands? Made sure cleaning items and food items are sterilized with each use and no cross contamination between your other pets occurs?
As these parasites can be transmitted from insects to dragons, changing your source of insects or getting a completely new batch could also help prevent reinfection from this source (or just have the insects checked to see if they are carriers).
Also, make sure your dragon is as stress free as possible, as his own body's defenses can also work with the medication to help fight off the parasites. Using the probiotic is good as well and make sure your dragon is well hydrated at all times, this deffinitely helps to protect his kidneys. Some parazap can be helpful as well (parazap won't necessary remove or kill parasites, but helps keep the natural benefical gut flora of your dragon in good health and they can help slow down or prevent harmful parasites causing problems).
This parasite doesn't seem to be very common with bearded dragons, I haven't seen anything mentioned about it in particular in any of the dragon books I have. I don't recall reading about it in the years I have been reading various posts etc about bearded dragons. As nobody here (or extremely few if there are any) are experts in dealing with internal parasites, it probably would be better for your Vet to use his resources to find other answers. Most vets know other vets who could lead them to new drugs or alternative treatments for entamoeba infections.
Worse comes to worse, he can do what I did and do a google search on entamoeba in reptiles. I found alot of hits, many written in pure scientificese which I am not very good at, nor patient enough to decypher LOL.
If your dragon right now is eating well and active, it may be fine to just leave things as they are and keep him as clean and healthy and stress free as you can. It is always possible he can fight off the remains of the entamoeba infection on his own. However, if he is lathargic and showing other symptons he is infected with parasites, a third treatment program may be necessary. Again I stress making sure you do everything possible to keep his cage and environment clean, clean and super clean.
