Hello Karen, sorry for not replying sooner but I was waiting to let someone else have a go.
I don't have any serious links between the Cubbington Skelchers and the North Oxon ones. In early days most other Warwickshire Skelchers are found in Mollington so are obviously part of the Banbury district kin, or are in the very far south of the county..
As you'll have read, most of the Cubbington Skelchers became Skelc(e)ys. No one has come up with a compelling reason why this should be so*, but either it's true or the Cubbington Skelchers died off or moved away and were replaced by Skelcys of unknown origin with coincidentally similar names and birthdates, who were born in Cubbington unrecorded.
One Skelcher who missed the name-change, probably because he moved away from Cubbington at the crucial time, was William Skelcher who settled in Hampton Lucy, having lived in Coventry. We don't know who his parents are but he was born in Cubbington about 1800, according to the 1851 on an entry that Ancestry has obviously transcribed as something else, because searching for it doesn't find it ( (HO 107 piece 2074 folio 831 page 1). Various descendants of his turn up all over the place - those that work as gamekeepers being particularly mobile.
The assumption is that the original Joseph Skelcher b about 1721 may have originated in North Oxon but who can say. One of his descendants Sarah, the daughter of William "Skelcher" Skelcey, did marry a John Dumbleton of Brailes about this time but I don't know if there's a connection.
Later Skelcher arrivals in mid-Warwickshire do tend to be born in the Banbury surrounds but some are unaccounted for. Have you noticed that in Northants the name Kelcher is commoner, which mirrors the tendency of Skelcey to become the (commoner) Kelsey, especially on the whim of the enumerator and particularly if the first name elides with its own S - cf Thomas or James.
The only suggestion I have other than Bishops transcripts prior to 1841 is parish records. They can be pretty unreadable too. There are some Skelchers on the IGI at familysearch.com
I know this doesn't answer many of your questions but I hope someone finds it of interest.
All best and Good Luck, Chris
*various theories on this: they couldn't spell so guessed, the enumerator hadn't heard of Skelcher but knew Skelcey, the name was originally German (Schelecher turns up a couple of times) and they changed it to avoid prejudice (though you'd think at the time anti-French sentiment would have been more likely) the brothers Thomas, John and possibly Joseph had spent time in North Warks where Skelcher is unknown but Skelcey occurs, so they acquired the names there and when they got back persuaded others to follow - which is why William "Skelcher" Skelcey dithers - christening his kids with both names, though they all end up as Skelcey (and some later become Kelsey but that's another story). One reason might have been because they found the name more euphonious than Skelcher, which does sound a bit awkward to me.
The North Warwickshire Skelceys seem to either go to Kelsey or disappear. It's just possible one or some of them end up in Cubbington, but I can't think what there was to draw them there, and one argument against is that this lot use a number of forenames - like Mark, Abraham and Benjamin - that are simply not found in Cubbington - there's a paucity of forenames with the boys nearly all called William John James George Thomas Henry or Joseph, with some Richard Edward or David and the odd Biblican oddity such as Imri (the forename of a local squire) or Enoch (named for a Mr Enock who married one of the sisters). The girls are mostly Mary Ann Hannah Sarah Emma Eliza(beth) Harriet Selina or (H)Ellen. Towards the end of the century they run out of names and get more inventive.
The first appearance of the form Skelcy in Cubbington is in 1807 when three births are registered, two to unwed mothers who match Skelcher sisters, and the third to a Thomas who doesn't. (None of these three children are ever reliably found again.) However there are Skelcher references after that including the marriage of Elizabeth Skelcher to John Enoch, and two payers of the Window Tax in 1817 - John and Thomas can only be the two old patriarchs at this stage, the others of those names are either too young or have left the village. However, by 1841 no-one is using the name in Cubbington.