OK, last post on this until you get back aghadowey, because I think your offer to try and sit and sort it all out is much needed!
1911 census, still in Fisher Street, Kinsale:
http://www.census.nationalarchives.ie/pages/1911/Cork/Kinsale_Urban/Fisher_Street/422939/Helena Savage is a Widow, age 72, H o H 47 years married, born 10 children, 6 of whom are living. All this fits with the death of John Savage, which Boobah has clarified (via the Fermanagh board) John died in 1909 age 75.
Living with Helena is her daughter Emma Frances, now 30. Again, all fits unless there are 2 almost identical John and Helena Savages in Cork, and I can't see another one.
Also living with her are the 2 grandchildren from 1901, Eleanor Savage Higgins and Edwards James Savage Higgins.
It's beginning to look to me as if Eleanor and James were the red herrings in the earlier confusion.
The gravestone that Mary found ages back in this thread showed the deaths of Helena, of Charlotte Anna Savage nee Higgins, who we now know was married to Richard Archibald Savage, and of her daughter Eleanor Frances Savage.
Aghadowey, your thoughts about another Higgins connection.. It's now obvious from the census in 1901 and 1911 that these two children weren't staying with grandparents, but living with them permanently. I still feel that the 2 families (census and gravestone) are one and the same family, but that there was a second Higgins connection that we haven't yet found that produced Eleanor and Edward, because it no longer looks as if they were Charlotte and Richard's children at all. All the rest of the family connections fit.
Would appreciate your thoughts before I tie myself up in even more knots!
p.s. once we get on the trail of these things they become irrestistible..if the children were living with their grandparents from such an early age (Eleanor was only a year old in the 1901 census) then it's likely that their mother had died.
Death: Eleanor HigginsQ. 1, 1900, Millstreet registration district, the same district as the children's birth registrations
Vol 5, p 482.
The death registration shows Eleanor's birth year as 1871.
One of the children of John Savage / Helena McCabe was listed as Elenor, born 27 Feb 1871.
I haven't managed to find a marriage for Eleanor to a Mr Higgins to support this, but as the death registration is the same quarter as the birth of the little girl, and the age of Eleanor, presumably dying during or immediately after childbirth, is correct for John and Helen'a daughter, I think you are right.
Two Savage-Higgins marriages.
Richard Archibald Savage married Charlotte Higgins, and their children grow up with the surname Savage. Charlotte is the Charlotte on the gravestone Mary found.
Eleanor Savage marries an unknown Mr Higgins, gives birth to Edward James Savage Higgins in 1898 and Eleanor Savage Higgins in 1900, and dies. That would be why these two children lived with their grandparents.
Does that make sense to you? because if it does we are looking at the same family.