Preview highlights disappear

I have the same problem on Monterey 12.2.1, MacBook Air and this is ridiculous, I lost 99% of my highlights in my pdf and I have to redo everything. Apple needs to fix this.

Give this a try: boot into Safe Mode according to How to use safe mode on your Mac and test to see if the problem persists. Reboot normally and test again.

NOTE: Safe Mode boot can take up to 3 - 5 minutes as it's doing the following; 

• Verifies your startup disk and attempts to repair directory issues, if needed

• Loads only required kernel extensions (prevents 3rd party kernel/extensions from loading)

• Prevents Startup Items and Login Items from opening automatically

• Disables user-installed fonts 

• Deletes font caches, kernel cache, and other system cache files

In all the years that I have been using Apple's Preview, I have never lost any annotations that I placed on PDFs.

I work on the boot drive filesystem, or iCloud Drive, but not on any third-party cloud service, mounted USB device, or share from a server. I don't attempt to rename or duplicate the PDF from within Preview, and depend on the autosave feature to update the PDF as I make the annotations (which one can see updated in the Finder Icon view of the PDF).

And to be current, none of the Preview annotations, including highlights, have been lost in macOS 12.2.

There are several, some long-running, in this Monterey forum of this same problem.

I am aware of that, but I have never experienced it, and the problems with lost annotation may be self-inflicted due to certain procedures or filesystem issues.