There are plenty of reports that a large deleted message box can slow you down, so what you suggest makes sense. I think it is "all or nothing" with the deletion. What I would suggest is that you go through the list, "retrieve" the messages you want to save (which will pull them back to your inbox) and then delete the remaining bulk of deleted messages. You can "re-delete" the ones in your inbox, if you want them kept in the deleted box for some reason.
Also remember that you have the option of setting a preference to delete everything in the deleted message box every time you log off, which will avoid this problem.
