To its current owners, the farmhouse had always been a curious mishmash. Crammed into its insides are 26 rooms and 13 staircases - creating a labyrinthine interior.
When Jane and Roger O'Brien bought the old farmhouse, 12 years ago, it was completely derelict and they did all the restoration work themselves - which gave them ample opportunity to uncover some of the contradictions of the building for themselves.
For example, the original fireplace had had five designs layered over the original, altogether more gaunt version that Jane finally revealed.
It was here, she thought, lay the greatest mystery - the fireplace seemed medieval.
But how, with such an elegant facade, could the original building have been medieval?
Perhaps the first owner had simply cannibalised spare parts from other disused and derelict properties?
Despite the elegant proportions, another bizarre aspect was that none of Church Farmhouse's windows are level - and there are plenty of small windows serving the myriad rooms in the upper parts of the house.
One interesting detail was in the pigsties. These were designed with some care, not to say style, in keeping with the seventeenth century design. The relative grandeur of the pigs' accommodation reflected their more elevated status at the time.
After sizing up different aspects of the house, however, it becomes clear that it was originally medieval.
The real breakthrough came in one of the bedrooms, which has an original medieval timber frame supporting the ceiling.
The County Records Office in Chester furnished proof, through the Kingston Estate Survey of 1665, that a medieval building had stood on the site before the farmhouse was rebuilt in the 1600s.
The trio of detectives found the person who transformed the building into its present shape, one Robert Wilson, who was a nonconformist and rebel who prospered under Cromwell's ascendancy, but subsequently landed in hot water as a dissenter on James II's return to the throne.
In 1683, Church Farm was searched for weapons and, in 1685, he was up before Chester Crown Court, as a "person dangerous to the government".
The team was also able to track down a copy of the will made by Robert's wife Ellen. That too grants a fascinating picture of life in this household as the eighteenth century begins. Among the items she bequests is a tobacco box, to her son Matthew.
The program illustrates to any house owner with a question about the history of their property how much of the evidence can be pieced together - both from the architectural detail and the local records offices.
'The House Detectives', Tuesday, 8pm, BBC2.