I am posting this here just to get a look from the server side, I have already posted this on the IOS side.
I have a client that has 1 user that is having an email issue. The issue is he has random emails that if viewed even for just a second on his IOS device will disappear from his IOS exchange box and from his Outlook on his desktop. Its very random and hard to know when it will happen. It just happened to him this morning with 3 random emails he received. We are running SBS 2008 with exchange 2007. I can look at the exchange logs and see where the emails hit the exchange server and were passed through just fine, but where they go when they disappear is a mystery.