Board Thread:Theories and Speculation/@comment-39350828-20200424153111/@comment-32685487-20200426030254

The eyeballs retain some of the users chakra hence the Sharingan Danzo had from Shisui retained Shisui's chakra and Ao pointed it out. Nagato's eyeballs were originally Madara's eyeballs so he would indeed have a bit of Six Paths Chakra in them still. Although there is remnant chakra in the eyeball, there is no proof to say it leaked in and mixed with Nagato's own Uzumaki chakra albeit it is possible.