"But I don't think that work well. The probiotic doesn't directly kill the supposedly bad guys, it just takes their resources and either prevents them from growing more, or starves them (slowly, as the probiotic takes hold). That doesn't (to me) sound like a process that can send enough killed bad guys into the bloodstream (where the anti-bodies can pick them up and over-react) fast enough to do what we know as herx. If there is another mechanism, then I'm all ears."
As I understand it, some of the soil bacteria or spores that are in some probiotics can cause diarrhea and other reactions because the flora of the gut is a cooperative ecosystem, and it puts up its defenses when new invaders appear. Its defenses include chemicals that cause diarrhea, because it wants to get rid of the invaders as soon as possible. It hides out in the biofilm, and the invaders are ejected.
Some of the microbes in the gut. such as Strep, I think, will throw out antigens as well as toxins that cause inflammation when they are killed. This will cause an immune reaction that makes you feel sick.
I think the bad reactions occur a lot more when the body's drainage system (the kidneys and gut) are not working properly, and some kind of toxins are stirred up.
Please correct me if I'm wrong about this.