Board Thread:Theories and Speculation/@comment-34661853-20181111160651/@comment-32685487-20181117215408

No, Nagato already had Madara's eyes in his head and in those eyes the Rinnegan was already there he just re-awakened them, and they didn't stay awakened. He had to re-awaken them again to protect Yahiko and that time they stayed since he was finally aware of them.