Im experiencing precisely the same issue. I have tried editing highlights with different PDF documents, I also updated macOS to 12.2, but the problem persists.
My only way to get rid of this issue is exhausting. I have to make a duplicate PDF (which has many of the highlights undone) and highlight them once more using the original (unsaved) document as a reference. Sometimes, the duplicate also has some highlights undone, so I have to repeat this process until all the highlights appear on the following duplicate PDF.
I want to continue using Preview as it's pretty seamless with macOS. I would appreciate some fix because this is making me go crazy.