Just had a 45 minute call with Apple, (which I didn't pay for!), ended up with a 'senior supervisor'. First guy said he had heard nothing on this issue. Senior supervisor suggested deleting the account and resetting - no good as I know some of the emails are no longer on my server, plus the issue is now affecting emails that are on my server! Also these emails are localised on the device so the server can not affect them. He said this sounds like an IMAP issue and was surprised at it being POP related.
Upshot is simple - if you have emails not on your server anymore that are lost on the device, they are gone and are never retrievable. Set your server to maximum retention would be my advice or move to exchange account! Sorry no good news.
The guy is looking into it from Apple's side and will apparently come back to me….