Well how do you think Hagoromo and Hamura damaged her in the first place?
But as I've said, I'm pretty sure Kakashi's Kamui Raikiri was in fact a Kamui imbued Raikiri....and not the black lightning Sasuke used.
Kakashi has already shown to be capable of using it that way when he made the Kamui Shuriken. So I think that makes more sense than him using a completely new technique that Kakashi was not known to possess.
Seeing as how she absorbed their chakra through Zetsu the first time maybe it's him that possesses the ability. And not her
Isn't chakra enhanced strength taijutsu?
No it wouldn't, Sage chakra is only Senjutsu and we see Nagato's path absorb massive Senjutsu imbued ninjutsus that pact more power than a simple Chidori. Sasuke's Amaterasu was absorbed just fine. Kamui is a a/t jutsu, it have no physical property, it was a Susanoo which is a physical form of chakra that used Kamui shuriken and on that form it can be absorbed. Kamui snipe forms a barrier around the target and Kamui intangibility warps parts or the whole body. Kakashi used senjutsus that Obito's chakra still had.