Board Thread:Naruto Discussions/@comment-29393962-20161111215453/@comment-25122992-20170117221535

See the explanation above, if databook says that souls do really reincarnate, then they must co-exist with the new vessel's soul. So no, Madara still had his own soul, but lost the soul of Indra which remained with him during his actual lifetime, yet has already gone to Sasuke at this moment (note: Sasuke still has his own soul as well). And yeah, chakra is here too, it can be a separate thing from the soul, but I also think that throughout the series it was implied soul and chakra are rather related terms.