I have the same problem. I spend days highlighting a Books document only to find my highlights suddenly disappear. Because it is a textbook, I can no longer efficiently review the material. When I contacted Apple Support a few months ago, I was told that that the problem *might* be the use of anti-virus software - I am not uninstalling that. Also, even though all settings are correctly configured, Books does not appear in my Time Machine - Apple had no solution for that. As a last resort, the Apple representative suggested I constantly close down and open the document as a way of *saving* the highlights, as there is no traditional "saving" function for Books documents. I did that this week, and it worked, only to find today - yet again - that the highlights suddenly disappeared. So, it appears that as an application, Apple's Books application cannot function as intended, and Apple does not have any idea how to fix that. I wish I had a solution to this problem, but I offer my experiences as a way of framing the issue in case someone else can provide a solution.