Based on past experience shared by others at this forum, these things just go away from time to time. They disappear for no apparent reason at all. And usually they just come back again all on their own, without any assistance from users at all. Most experiences shared here at the forum say this problem usually resolves itself within a few days.
I believe that those who use highlights, tags, notes, etc., exercise great faith. And from what I have seen, their faith has been rewarded. I, on the other hand, am one of little faith in this regard. Because of what I have seen and heard, I have never chosen to use any of the highlighting, tags, notes, or any of the other things that might aid me as I study the scriptures and other materials in Gospel Library. I use other methods and means of recording the thoughts and revelations that are so personally important to me.
To set your mind a little bit at ease, I have surmised over time that things such as your highlights, tags, notes, etc., are still there. I personally believe the problem is caused when the servers at Church headquarters get confused from time to time as they sync with and talk to our devices at home, and everything goes away until the servers and devices agree once again on how to speak civilly with each other.
I have never had a piece of paper reboot while I was giving a talk or leading a discussion or lesson. On the other hand, I think that is all that is happening here with your highlights, etc. It just seems to take longer than a simple reboot for everything to get back together again.
I have other ways of learning patience that do not involve the fear of losing my most valuable creations.