I’m concerned I'm not getting all the protozoa and worms out before the reseeding phase. Will the botanicals for the path purge continue to work in the body to get any worms out after I’m done taking them?

Yes, they will continue to work, and the reseeding supplements will also root out the worms. Take your clay/earth until they are finished. If you are truly concerned (they could be small worms— if you aren’t seeing them in the toilet, it doesn’t mean they aren’t evacuating), you can continue the Medi-Clay and Diatomaceous Earth during the reseeding phase without compromising anything.