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This came up in my last game with my Necrons and didn't know how to rule it.

I had two squads of warriors and one got completely wiped out, but made their WBB rolls on account of the other warriors being within 6". Now the question I have is, is the downed squad worth a kill point for annihilation missions or no because they got back up with another squad?

In the codex, it talks about about victory points and we ruled along those rules but modified it for kill points. Whats your take?

The squad that the former Necrons were in is now dead. So, your opponent gets 1 KP.

The unit no longer exists, as they have all joined other unit(s)

The downed squad counts for a KP, even though some members phased into another nearby squad.

furthermore, if they are down at the end of the game, they count as a KP.