When syncing mobile devices you have to choose which devices have priority.
When the appointments on the server were made, you synced the blackberry…it then accepted those appointments and added it to the blackberry’s calendar. You then got rid of the appointments on the server, and after syncing, the server calendar now copied the ones on the blackberry. There is a setting (forgive me for not being able to tell exactly how to find it, as I am not by our server), that tells you which device has priority for that sort of thing.
Hope this helps!