The first hint we really get of it is at the end of Batwoman #18, where Bones releases Alice - Beth Kane, Kate's twin sister, Bette's cousin - from where he's been keeping her and the first thing he tells her is "you have our sisters eyes", which echoes what Alice says to Kate at the end of Batman #857 during her big reveal: "you have our father's eyes"

Then in the next issue, Jacob is talking to Catherine Hamilton, who has found out about Bette being Hawkfire and Kate being Batwoman, and she's angry and terrified that Jacob is going to get those girls killed. (It's a wonderful reframing of Catherine, who until then had mostly been seen as a snobby socialite.)

Batwoman was undergoing BTS issues around this time - the character had proposed to Maggie Sawyer, but DC was firmly anti-married couples, so the creative team was leaving the book and Marc Andreyko was taking over, so the arc gets pushed from the main book to Batwoman Annual #1

Interestingly, you can already see the change above, where Jacob tells Bones he's not his son - and it looks like Jacob no longer believes he ever had a son. (Which is...fine by me? Batman and the Wayne branch are so male-centric, I'm glad for the Kane branch to focus on the Kane women.)

It turns out that Bones was unstable and believed Kane to be his dad, but his dad had actually just served with Kane back in the day. Which is all well and good, but it never explains WHY Jacob Kane thought he had a long-lost son somewhere.

comics!

I really do wonder, though, if the creative team had never changed, whether or not Bones WAS going to be a long-lost brother to the Kane twins. That would have been...interesting? Part of me is really glad it never happened, but part of me is VERY curious about where the story was intended to go, because it was packed away so quickly.

repeatandfade: COMICS!

I should point out that the annual where the story was wrapped up/washed away was written by Andreyko, whereas the other stuff was written by JH Williams III and W Haden Blackman

(Also, I'm particularly irritated by the annual in that you have Bette in the same room as Batgirl and Nightwing, but they never cross paths in the story.)