The caulking is cosmetic. If the floor is discoloring, then the wax ring stuff has either failed or was not installed properly, and the seal is leaking. : my husband put in new flooring and took our toilet out. when he put it back in he put that ring stuff on and set the toilet on top of that seal. he then caulked the outside of the toilet. (hes gone) this caulking has come up and i dont know if i should replace this? the flooring seems to be rotting around the toilet. what should i do first?