There seem to be all sorts of questions here.
Were the two children actually children of the marriage? The fact that Alexander, on his death, leaves all to a niece, implies either the children predeceased him, or that there was a major family rift, or that they never were his children and when Paddy left (I am assuming when you say she went up north, she went alone and separated from Alex) he lost all contact with them.
The other question that I cant help thinking of, is - does it really matter? If you are following the Lewis line, then going backwards from Alex you will be OK, as it will be the same as your own line. Going forwards - well, there are no registrations for children of the names you have given under Lewis, so it does look (coupled with the lack of provision for them in his will) as if possibly they were never Alex's children. If they were, then it is them that need concentrating on, from a genealogical point of view, rather than the elusive "paddy".
With no obvious marriage to be found, no childrens birth under Lewis, no mention of children in his will, no family contact or knowledge of any children ....... I would guess (and it is only a guess) that they were Paddy's children, and at the time you met them Alex was 'friends' with Paddy. This may be that they were together as a couple, but may not. I guess you were only young at the time you met them, so the exact nature of the relationship may not have been clear.
