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. And yeah, chakra is here as well, it can be a separate thing from the soul, but I think that throughout the series it was implied that soul and chakra are somehow related terms.