I am also experiencing this issue with PDFs of all sizes. It's happening on Windows client on every machine I use. I don't use annotations on mobile, so I can't attest to wether it's also happening on Android.
The issue seems to occur on saving the PDF after a considerable amount of new annotations have been added.
As mentioned by BasieBand, the annotated PDF still seems to exist on the note, as saving the note's attachments produces it out of thin air.
I honestly don't know how to stress how critical this bug is. It should be obvious.
Hoping for a swift fix, as this is killing my workflow.