I understand the reseeding phase is building the microbiome, but what if there are still worms in the body?

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.