I just upgraded to Office 2016 via the Office 365 subscription. Working on a Surface Pro 3 and Windows 10. I am mostly using OneNote 2016 to take handwritten notes using the Surface Pen.
The disappearing ink issue, (that was a problem in the OneNote 2013 edition, until it was fixed), seems to be back: parts of written stuff disappear. I was writing in OneNote 2016, and out of nowhere, parts of what I had written earlier disappeared. Though the issue is not as severe as it was earlier, when the disappearing was very frequent.
This needs to be fixed ASAP, it renders OneNote not very useful for note-taking!