Board Thread:Theories and Speculation/@comment-1512913-20160329065033/@comment-5936871-20160404195719

Yes, he received Hashirama's cells from Kabuto so he has both Asura and Indra's chakra as well as Hagoromo's chakra that he gave him. Hashirama's cells still have Asura's chakra because Madara's body still has all of the chakras. This is proven when we see Hagoromo arise from Madara's lower half stating he was able to arise because of Kurama, Asura, and Indra's chakra all in one place.

If the chakra moved on how would Madara even still have his Rinnegan? It should revert back to EMS cause he'd lose both chakras. It probably just replicates itself and then moves on.