Complex sentence: The Qualified Congregation joined the Scottish Episcopal Church in 1803, but it took a further twelve years for them to amalgamate in a union whereupon they moved back into the old Qualified Chapel, this time as a full-fledged congregation of the Episcopal Church.
Split into simpler sentences: The Qualified Congregation joined the Scottish Episcopal Church in 1803, but it took a further twelve years for them to amalgamate in a union. Whereupon in 1815 they removed back into the old Qualified Chapel once again, this time as a full-fledged congregation of the Scottish Episcopal Church.