I'm very sorry your dragon is sick and has MBD, but there are a lot of things that we can help you with here, in fact we can most likely help you quite a bit more than most vets can, especially if your vet is not a Board Certified Reptile Vet. Unfortunately, most "exotics" vets know very little to nothing about bearded dragons, and even less about proper husbandry for them. It sounds like you've got some husbandry issues, the first being the "bark"...are you talking about "bark" as in you've been using loose bark as the substrate in the bottom of her enclosure? If so then yes, you absolutely must remove all of it for a number of reasons....Is there any way you can post some photos of both PeaTree and then her enclosure and lighting? That would be extremely helpful for us...also, it is not generally a good idea to use a Heat Rock with bearded dragons at all, first off dragons get all of their heat from light coming from above them, that's where their heat needs to come from, a bright white basking bulb that puts their temperature gradient within the correct ranges, and secondly bearded dragons often burn their bellies if they have a Heat Rock because they don't really respond to the heat underneath them at all. It's not uncommon for a bearded dragon to have damaged scales on their belly due to a prior heat rock. So you're best to unplug the heat rock, if she uses it you can keep it in her enclosure, just unplug it, and make sure that she is getting her enclosure to proper temps by using the correct wattage, bright white basking bulb.
Just as an FYI, bearded dragons come from the Australian Desert, which is very hard, rocky terrain and actually has very little sand, gravel, or any loose substrate. Bearded dragons lick EVERYTHING, that's one of the ways that they feel things, with their tongues, and as such if you have any loose type of substrate inside their enclosures they do in fact end up ingesting some of it, it's inevitable, and this always becomes a problem, as they do not have the gastrointestinal tracts to handle anything that they cannot break down and digest. In addition, all loose substrates are perfect harbors for bacteria, fungi, parasites, and pretty much all harmful microbes. They move into and throughout the loose substrates and then breed in them, and this results in most commonly skin infections in bearded dragons, including Yellow Fungus, which is pretty much incurable and lethal, as well as upper respiratory infections, eye infections, and scale rot. So most all experienced bearded dragon owners and breeders are fully against using any type of loose substrate inside the enclosures of bearded dragons, and instead use only SOLID SUBSTRATES, like stick-on textured slate floor tiles, non-adhesive shelf liners, carpeting, and even just newspaper or paper towels, which can be thrown out and replaced with fresh when they become soiled. So yes, please remove all of the bark from your dragon's enclosure, completely disinfect the entire tank and everything inside it with very hot water and either bleach, Hibiclens, or F10 Reptile Disinfectant, and then you can put down clean, dry paper towels in the meantime while you decide what you want to use as a permanent, solid substrate...
Now that we got that out of the way, if you could answer some questions about PeaTree it will help us figure out what's going on with her and how to help her...First of all, how old is PeaTree? How long have you had her? Did she come to you already having the MBD, or did she develop the MBD while with you? The biggest factor that causes MBD in bearded dragons in not a lack of calcium in their diet or their owners not dusting their live insects in calcium and multivitamin powders, but rather the owners using either no
UVB light at all, or more commonly they are using a
UVB light that is not at all adequate for a bearded dragon, and that is typically not mounted correctly in the dragon's enclosure (usually the
UVB light is being blocked by a mesh lid or a clear plastic cover on the UVB tube fixture) or within a distance of the dragon's main basking spot that allows the dragon to absorb adequate
UVB light while basking.
Unfortunately, about 90% of the UVB lights that are sold are not at all adequate for a desert reptile like a bearded dragon, even most of the UVB lights that are labeled as being for bearded dragons are in fact far too weak to emit adequate
UVB light for a dragon. So all of the calcium that the dragons take in through their food, all of the calcium dusting of insects, and any liquid calcium supplement or calcium injections given by vets are essentially worthless if the dragon is not under an adequate UVB tube that is mounted in the enclosure unobstructed, and within a distance that allows an effective amount of UVB to reach the dragon while basking for at least 13-14 hours every single day, along with a bright white basking light that is putting their temperature zones/gradient within the correct ranges.
UVB light allows dragons to manufacture their own, natural Vitamin D3, which in turn allows the dragon to absorb and process any and all nutrition that they take in, whether it be food or supplements. So without 13-14 hours of adequate wavelength and strength of
UVB light every single day, and without the temperature gradient/zones being within the correct temperature ranges, basically the dragon cannot absorb, process, or use any nutritional content, vitamins, minerals, enzymes/amino acids, etc. that they are taking in, and this results in very weak bone density, malnutrition, and nutritional deficiency diseases like MBD and Vitamin B1 deficiency disease. It also causes them to have a complete lack of appetite and to become extremely lethargic.
So while the vet visit and the calcium injection certainly caused your dragon some stress, which should resolve itself within a few days of her being home, if you haven't corrected any husbandry issues like getting an adequate UVB tube that is mounted correctly, using a bright white basking bulb that puts her Main Basking Spot Surface Temperature, the Hot Side Ambient Temperature, and the Cool Side Ambient temperature within the correct ranges, and having both of these lights right alongside each other and directly over her Main Basking Spot within the Hot Side of the enclosure, she will continue to not have any appetite and be lethargic, and the calcium injection she got will not do any good at all. The only way to stop the progression of MBD and hopefully reverse at least some of the disability caused by the MBD is to get the husbandry that caused the MBD corrected. So whether she came to you with the MBD (I don't know her history yet) recently, or whether she developed while she was with you, she needs correct husbandry in order to get back on track.