PDF files randomly get deleted

I have sync set up on my computer and ipad. I have pdfs that I annotate using my ipad and then later view on my laptop. When trying to do this eariler, I had found that some of my pdfs, with annotations had been deleted, by my ipad - I did not do this. I also can’t restore them. Why is this, and are there any fixes to this?

What, if any, plugins do you have installed?