I did some more testing, this time watching the files in Google Drive also.
[ The description of the test refers to the android “back” (looks like <) button and “home” navigation buttons (looks like a rounded square).
After annotating, the back button returns from the pdf to the paperpile entry for that paper (the one with biblio info for that paper), whereas the “home” button goes to the main android “desktop” screen. ]
It seems like one fairly reliable way to cause the missing annotations is to click the android “home” button after creating an annotation (rather than clicking the back button). Then on the desktop, after clicking paperpile and re-opening the pdf, all annotations are missing, both previous ones and the most recently made one.
However, on Google drive what I see is that all the previously made annotations do exist, and only the most recent one (the one followed by the home-button click) is missing. So the problem is both that it is not saving annotations sometimes, but also in some other cases it does not display annotations that exist on drive.
After exiting and reentering Paperpile some random number of times the previous annotations reappear, but the most recent one (which was followed by the ‘home’ click) is permanently gone.