To be clear, this is a self-inflicted wound by the user. They are reading a topic, then the notification they click or tap on, jumps them forward in the topic.
We always track the “lowest” or “bottom” reading position in a topic. That’s what the little back button does on the vertical timeline. We don’t track “reading holes” primarily because it becomes a UI nightmare 
About the best I can think of is a dialog that says “are you sure you want to jump forward in this topic and lose your place?” when you initiate navigation to a lower / deeper post in the topic. That might be just as annoying, though, if not more annoying, than losing your place .. I’m not sure?