Board Thread:Theories and Speculation/@comment-30355627-20161218164138/@comment-1512913-20161221225259

Yes it did, Momoshiki. The only reason why Madara and Sasuke also come with Sharingan besides Rinnegan is because Hagoromo most likely had Sharingan as well besides Rinnegan and that power was passed onto Indra. Obtaining the Rinnegan while having Sharingan doesn't make the Sharingan disappear, but the Sharingan is not what changes into Rinnegan. They are separate doujutsu, both present and usable independently on each other.