@Csound. all,due respect you post a lot.,but does it matter if it was bad coding or sunspots? the problem seems from the outpouring of conversation and AppleCare Tier 2's input that it began with iOS 9. i never had this with any previous iOS.
ALso where do you draw the line? This issue might not effect every user, but in my observation, I'm finding it intermittent and thus hard to know the troubleshooting circumstances. as with most intermittent issues, feel has a part and I feel that the issue may occur when an email is downloaded to multiple devices or computers. im thinking it may be if I download on my iPad which leaves the original on server, then download on my Mac Pro which does delete off server on dnld and then I can't see the entir message on iPad as if the POP email didnt dnld in the first place and was acting more like IMAP and when the original POP was deleted off server, iPad couldn't find the original again.
THis is is making more observational sense, but I can easily troubleshoot this scenario and will hopefully later today.
but your point about every user, in this case is problematic, because it doesn't even effect those that report having the problem every time. So since the perfect storm is needed, I bet there are users who don't know the problem is lurking for them.