Ok , been playing with the possibilities this is a Outlook issue. I experimented with outlook and was able to cause this issue to duplicate (at least I lost email) on the BB. When I set the outlook to save the emails in a folder other than the default folder on my Pc, when Outlook moved it from the server default location it also disappeared from the BB. This is not easy to understand why but it may be a weird anomaly in the wireless connection between Outlook and the BB. Using this findings as a search issue at RIM I discovered they do have an issue with email being placed in a .pst file and deleted.
Read the attached link and maybe it will help.
KB20391-Email messages are deleted wirelessly after they arrive on the BlackBerry smartphone