AD is not the problem as far as what's going with Exchange as I found out from talking with Microsoft's PSS who I think know better. The problem is that when you remove AD from a Exchange box it changes the permissions on .net which Exchange sets up when installed initially. The only short way to fix it is to move the mailboxes and uninstall Exchange then reinstall Exchange using the /disasterrecovery option.

My question still stands regarding how BES intergrates with Exchange, and if I where to build a new Exchange box and move the old mailboxes over before nuking the current Exchange does it effect BES if so how? Or what do I need to do?

Thanks
Andrew