He then declined to take them, but remained in possession of his posts until 1 August 1690, when he was suspended from performing his ecclesiastical functions until 1 February 1691, then formally deprived.
In 1692 William Sancroft, the deprived archbishop, formally delegated to Lloyd as his proxy in exercising his archiepiscopal powers in spiritual matters.
Lloyd signed two published letters, one A Vindication of the [nonjuring] Bishops, 1690, and another appealing to all Christian people for assistance to the suffering non-juring clergy, in July 1695.
When a list of non-juring clergy was taken to James II at the Château de Saint-Germain-en-Laye, the exiled king directed Sancroft and Lloyd each to nominate one suspended clergyman for the episcopate.
His death was followed by the return of Henry Dodwell, Robert Nelson, Brokesby and others to the national church, Ken having expressly declared a wish for the schism to end.