As @KAZ_NZ mentioned I believe this relates to the following apple kb article support.apple.com/kb/TS4511.
Unfortunately the mitigation steps have not helped and we still require a solution.
The mailbox in question is 10gb, and contains about 10 years of emails, but the user does not want to split or archive this.
He has 3 ios devices on him at all times, sometimes the problem occurs on one of them, sometimes multiple, but each time it does occur it takes hours and hours to get them all back.
If this really is as unresolvable as it seems I would at least like to know if we can alter the way the emails are reloaded onto the device, at the moment they come in oldest to newest, but I would prefer the reverse.
Also is there not just a way of turning off what appears to be a security feature:
indication that something's wrong with the server and that the validity of data it previously cached is suspect.