It seems that there could be some random behaviour in play with the PDF annotation functionality in Moodle.
In an assignment with 44 submissions 3 of them are experiencing a problem with missing content on an annotated PDF - the downloadable annotated PDF files only contain the annotations but no original content.
Up to now this problem has appeared only with assignments that have multiple attempts and the problems are apparent only on the first attempt.

Could this behavior be inspected in more detail and analyzed?