Do you happen to know offhand whether the papacy formally dissolved and suspended the Catholic dioceses in the interim, or did the Vatican establish an episcopacy in exile of some sort?
Whoever occupied the throne filled episcopal vacancies with persons sympathetic to his/her convictions and policies much like the Supreme Court today (in a few cases, non conforming bishops were removed via the bonfire). Henry VIII appointed pre-Lateran minded Catholics, Edward VI appointed staunch Protestants, Mary I appointed Catholics and Elizabeth I appointed mild Protestants or "Anglicans". There never was a wholesale "cleaning out of the episcopacy" by any king or queen. Around 1582, the Pope excommunicated Elizabeth I and all who were loyal to her (to my knowledge, this, the final breach between the Anglicans and Catholics, still stands and that therefore, according to Roman Catholicism, all Anglicans are going to hell). I do not know if any of Mary I's bishops were still around at the time. If there were, they were eventually succeeded by Anglicans. The attempt by Spain (with Papal support) to solve the problem by force of arms failed.
To answer your question, because the dioceses in England were led by men loyal to Elizabeth I, they were tossed out of the Catholic Church. In recent centuries, the Catholic Church established new dioceses (new names, new cathedrals, new boundaries) for the loyal Catholics in England. Should a reconciliation ever be forged between England and Rome, it would be interesting to see how the historic dioceses and the new dioceses would be settled.