Tutorial Link: http://wiki.bf2s.com/tactical-guides/editing-favourites
Well, I just figured one way to do it that works. Less elegant than the tutorial link above but it worked for me. I went into the Battlefield 2 folder in My Documents and navigated to Profiles/001 folder In there I cut and saved the files labeled for my video, audio, and control configs. to a folder on my desktop. Now next time I ran BF2 I had to retrieve my account because of what I cut/deleted and start the multiplayer game. This created a new profile folder 002 with a blank favorites menu. I took all the files from that folder and overwrote/copied them to folder 001 and deleted folder 002. Then I took my original video, audio, and controls files I previously saved to a folder on my desktop and copied them/overwrote to the 001 folder. I have all my original settings except now my favorites menu is a clean slate.
Well, I just figured one way to do it that works. Less elegant than the tutorial link above but it worked for me. I went into the Battlefield 2 folder in My Documents and navigated to Profiles/001 folder In there I cut and saved the files labeled for my video, audio, and control configs. to a folder on my desktop. Now next time I ran BF2 I had to retrieve my account because of what I cut/deleted and start the multiplayer game. This created a new profile folder 002 with a blank favorites menu. I took all the files from that folder and overwrote/copied them to folder 001 and deleted folder 002. Then I took my original video, audio, and controls files I previously saved to a folder on my desktop and copied them/overwrote to the 001 folder. I have all my original settings except now my favorites menu is a clean slate.