In short, St. Elsewhere ended with the revelation that the events in the series were the dream of an autistic kid named Tommy Westphall.
This implies that various characters who crossed over into St. Elsewhere or other references to St. Elsewhere were also in Tommy Westphall's dream. Therefore, the series containing those characters and events must not exist, save in Tommy Westphall's dream.
This slightly faulty logic has staggering implications.