II've held off replying until I have given sufficient time post the 9.1 update to confirm we are clear. Here are my observations:
1. We have update an iPhone 6, iPhone 5c iPad 3 and iPad Air 2 To 9.1. All we're exhibiting identical symptoms post upgrade to iOS 9. All our email accounts are pop.
2. I have had iOS 9.1 running on my iPhone 6 since last night. All emails that I have received today are still present. There have been no cases of "this message has not been downloaded from the server" in any of the emails received post update.
3. Unsurprisingly older messages already affected have not been recovered.
4. I noticed a lag when opening emails with graphics or pictures. When I select airplane mode the email text is unaffected but the pictures are not shown only the empty frame placeholder. I can confirm that data is being used to download these images (from where? More to follow).
5. Attachments such as PDFs are not affected by lack of a data service (good news) so whilst not pretty pop emails are once again functional when off the grid (important for me in a rural area).
6. When I got home I downloaded today's emails to the computer which removes them from the email provider server. all of today's emails were still accessible despite the original no longer being present in the email provider server or any of the folders. I even turned the iMac off so there could be no weird back channel to the only other version of the email.
7. When I select airplane mode the pictures in emails still disappear, when I select airplane mode off the pictures reappear with a slight data usage (difficult to attribute categorically) where is this data being cached???
in summary - based on a sample of one uk email provider (BT) and 4 iOS devices from iPad 3 iPhone 5c to iPhone 6 iPad Air 2, pop/smttp email is functional again on iOS 9.1. Text and attachments appear to remain on the device even when data connection is lost and the email is no longer available on the server. Something has definitely changed and it's certainly not pretty, I'm also a little concerned that my email is being stored in another location. So good news with caveats