After spending a long time trying to figure this out and writing this post I found a solution. I’m posting anyway so that if anyone else has this problem there will be a solution for them to find.
What I’m trying to do
My highlights are not showing. Meaning when in edit mode in live preview, the words that are highlighted appear as normal unhighlighted words. If you go to that word you will see the == before and after but once you click on a different word they disappear completely and the word(s) is not highlighted. In Reading mode I do see the highlights. I used to see them in Edit with Live Preview mode but it’s just not there anymore. I’ve tried a whole bunch of things and cannot find an answer. I’ve searched here and on reddit too and nothing seems to come up.
Solution
I turned off all community plugins and highlights started working again so I selectively turned the plugins back on one by one. I found that the Enhanced Annotations plugin is what is causing this issue. Once I turned it off my highlights show up again. Hopefully this helps someone.