I know what you mean, it's frustrating!
others may have different opinions or strategies, but with a lifetime of medicating reptiles and having the same issue with most of those pets, I have personally found it best to only handle them when medicating them for the duration of therapy, and then when it's all over wait a few days and start your normal routine slowly again. I know that you mean well via the other option, but most herps and particularly high-stress ones like chams just won't "get it", and will usually just stress more. which doesn't help the disease or your relationship. you can think of it as their short term memory is there, but the long term memory is not. so they will be pretty unhappy now while treating, but when it's done and you are then consistently handling again without medicating, they typically calm down and relax again in my experience.