The thread of
https://www.mobileread.com/forums/sh...d.php?t=309966 sounds like they have discovered the common reason for both issues.
However, the provided "ps"-command did not result in a PDF document that displays the handwritten annotations on my Debian machine.
The mentioned PDFedit flattening I could not test. PDFedit seems to be unmaintained since 2012 and probably dropped out of Debian some time ago. There are no deb-packages I could find.