PDF editing in preview not saving changes

When using the markup and edit features in the PDF preview, it's consistently not saving changes I make. But only in particular sections. I will manually save (command s) multiple times but some changes won't save. Certain sections of the pdf will delete highlights and notes, even if other sections retain my edits. I check the 'revert' options and even the 'new' saves that are timestamped after I make changes won't show them. And if I make a duplicate copy of the pdf similarly some edits won't be there.

I thought maybe the system just needed more time to recognize the changes, but even after it being open a couple hours if I save again the changes to certain sections are still deleted from new saves.

I am so confused and very frustrated, it's deleted part of my work several times by now.