I've been fighting with this problem since it started. My wife, who was in Europe and did NOT upgrade to ios 9 until she returned, said that she was starting to lose email content BEFORE the upgrade.
A long conversation today with Apple senior support blamed the whole thing on my IP provider, Road Runner. I then spoke with RR level 3 and they said that my pop-server was configured correctly and it was Apple's fault. It is possible that the IOS9 upgraded did a default search for my email accounts and set up everything as IMAP, but RR said that the settings would then have changed. In other words, there is no way that my particular settings (especially the port) would access the IMAP server.
A few things are clear. If you delete and restore a RR account, it will default to IMAP and not give the opportunity to change it to POP. If you set up a new account, you have the POP alternative. You can use the garbage input discussed above to set up a new POP account and then put in the old account data after the new account is rejected, but that deletes all the place holders. I do not believe this will stop the content deletions; I'll know more tomorrow.
Content deletions are entirely random both as to time, size and what is deleted. I've reported this bug to Apple on a daily basis but have not received a response.