I second that the issue seemed to have started when the new iOS upgrade came out a few weeks ago. I just sent in my activity logs from both iOS and Mac so hopefully it gets resolved soon. Here are some problems I've had.
When I make highlights on my iPad, they just don't transfer to my Mac. So I re-highlight on my Mac......but then some of those highlights I made on my Mac won't appear on my iPad version.
After re-highlighting on my Mac, maybe a few days, maybe hours later, poof, all the highlights I made are gone. I've done the same note multiple times now, and won't be doing it again until there's an update(s) on iOS and Mac because it's just a waste of time.