As Stone began what would become his decade-long episcopate, Allen moved to Ohio (by its constitution a slavery-free state), where he became a missionary under Bishop Philander Chase.
[9] Allen then moved to Cincinnati, where he revitalized Trinity Church in 1844, but three years later the congregation had difficulty meeting its mortgage payments.
Andrew White and others and the ensuing sectarian violence, ultimately resolved in a policy of religious toleration among Anglicans, Catholics, Presbyterians and others as documented in acts of the Maryland colonial Assembly session of 1649.
His history of Shrewsbury Parish in Cecil County was prefaced by a quote from Ecclesiasticus XLIV:9-10, "And some there be who have no memorial ... but these were merciful men, whose righteousness hath not been forgotten.
A descendant, Col. William Allen, principal of McDonogh School near his former Garrison Forest Parish, attempted to edit his papers.
After the Civil War, Allen moved to Kentucky, from where on December 31, 1869, he advised Bishop Whittingham about the controversy surrounding the Diocese of Kentucky's assistant bishop, George David Cummins, whose fervent opposition to the Anglo-Catholicism of the Oxford Movement eventually led him to withdraw from the Episcopal Church and found the Reformed Episcopal Church.
In 1869, the Diocese of Maryland bought many records that Allen had preserved, which with Bishop Whittingham's papers, remain at the diocesan archives in Baltimore.