I'm sorry she's been having these issues for so long, but they should both be easily taken care of if the vet treating her knows what they are doing...is your current vet a reptile specialist, or an exotics vet? Did they tell you on either the first fecal test or the second, or both fecal tests what her pinworm count or load was? And what medication did she take the first time, and what doseage for how long?
As far as the pseudomonas goes, did they tell you what her count or load was of it? And what dose of Baytril did they give you to treat it, and for how long?
Lot of questions, I know, lol...lastly, what symptoms was she having or is she still having that lead you to take her to the vet initially in the first place, when they did the first fecal and diagnosed her with pinworms? Have those symptoms improved at all since she finished the first round of meds? Or have her symptoms gotten continuously worse? Have you been giving her probiotics too this entire time?
Here's the deal: there's a reason you took her to the vet in the first place, so she must have been having either runny, very smelly stools, or a low appetite, or lethargy, or a combination of all of these, or maybe you even saw the pinworms in her poop. That being said, pinworms are not at all uncommon in reptiles, and a lot of vets will treat for pinworms with a very harsh med that can actually cause more problems than the poor thing had to begin with. Also, if they prescribed the wrong medication for the pinworms the first time around then this first med only served to make her feel worse. I'm going to assume that she has a high amount of pinworms and that's what has been causing her symptoms this entire time, and that the first vet just prescribed an ineffective medication the first time around, and probably did not give you probiotics to give her, so the first medication probably made her gastrointestinal system all out of whack in addition to not getting rid of the pinworms. So now she's actually worse, which is to be expected. As long as the medication she's NOW ON for the PINWORMS is the correct medication, and you start giving her probiotics daily along with the pinworm medication, she should start feeling better soon.
I don't think that the Pseudomonas is causing any issues at all in her, and Baytril is definitely not the correct drug to treat it even if it does need treated. Baytril is THE GO-TO broad-spectrum antibiotic for vets treating reptiles, but it's not going to be effective at all for Pseudomonas, nor does she probably need ANY treatment for the Pseudomonas. Pseudomonas is an opportunistic bacteria that is usually found in the stool of all reptiles, and it usually causes absolutely no issues at all UNLESS the dragon has an already existing immune system deficiency or other serious health problem or condition that is compromising her immune system. Only then will Pseudomonas cause any symptoms in a reptile or need to be treated. I know you said she's a rescue, so I have to ask, does she have any serious health issues, diagnosed diseases, or anything else going on that is compromising her immune system? If so, then if the Pseudomonas count is very high, and ONLY if they do blood work to confirm that a bacterial infection is causing her white blood cells to be very elevated (a fecal to detect a level of Pseudomonas that will cause an infection that needs to be treated is not something to medicate on, only blood work), then I'd medicate her to treat the Pseudomonas, but only then, and I would not prescribe Baytril at all as it won't treat it, they should prescribe Cefotaxime.
But again, I would never decide to treat a Pseudomonas infection based on finding it in a fecal test, as finding Pseudomonas on a fecal test does not at all tell you whether the Pseudomonas is causing any problems she is experiencing at all, only blood work will do that. And since she also has pinworms, which if detected on a fecal test in a high enough amount will absolutely cause her problems, I would only treat the pinworms with the appropriate medication, and definitely would not give her the Baytril at all.