If I had the problem you have mentioned, I would probably do a couple of things to try to resolve it.
First and formost -- make backup of both BB and of the Outlook contacts. This will ensure you can recover if things screw up again. (I've never done it, but from what I've read here, you can do a selective restore of parts of your BB backup, such as just the contacts.)
I would create a new Outlook contacts list and do a one-way sync from the blackberry to that instead of my regular contacts list (create one called something like BB Contacts). You will have two separate Outlook Contacts lists. I would then do a side by side compare of the two and missing info from the BB contacts list into the regular Outlook contacts - edit until you are satisfied that the Outlook contacts list contains everything from both. This may take a little while but once you get the contact list cleaned up in Outlook on the PC, you should be in good shape for future.
After you are sure the Outlook contacts are done, delete all contacts off of the BB. Now do a one-way sync from Outlook to the BB and you should be in good shape. After that, always do a two way sync and it should keep both in line.
Sounds like what you thought would happen was that syncing would MERGE the contacts. But it doesn't work like that. It also sounds like the settings were for Outlook to overwrite the BB -- you can control this as well. If you look under Conflict Resolution (under advanced in Synchronization settings), your choices are Add all conflicting items; ignore all conflicting items; notify me when conflict occurs; device wins; or Microsoft Outlook wins. It sounds like yours is set so that Outlook wins -- I keep mine set to notify me.
Hope this makes sense and helps.
Personal: iPhone on AT&T
Work: BB 9650 on Sprint