Hi Liz
Let me see we have this correct...
We have established that your Grandfather was Robert Henry Cain and he had a sister Lilian and their parents were John Henry Cain and Edith Cowle. (Your Grandfathers WW1 record also confirmed his parents as John and Edith - one record mentioned sister Lilian and another referred to her as Lydia- so maybe Lydia was her name but called Lily). What you need to go back further is the Fathers name of John Henry which looks like will only be obtainable from the Marriage Certificate of John Henry and Edith. Now, maybe someone can correct me here but I thought from BMD you only got the name of the bride and groom, quarter and year they married and the district/page/folio number which you then used to obtain the actual certificate - in short BMD doesnt give grooms Fathers name. On the other hand if you look on LancashireBMD it also gives the name of the Church. If your nephew looked at the actual Church records that would give the Fathers name..but.. didnt he think John Henry Cains Father was Jonathon which we have discounted as his son was John Hubert? So, to round off, if he did have John Henry Cains and Edith Cowles Marriage Certificate but his Father wasnt Jonathon..he thought he had the wrong one! So the name he has as the Father WILL be the correct one we need to look for.
Hope that makes sense!
Will have another look for 1891 Census for you.
Sandra