When I started taking over the Mantis operation for our tournaments, I noticed a similar problem.
I closed all tournaments and reported/uploaded them (some had been around for a very long time like yours). UDE took them into their rankings database as far as I could tell.
Now the only time I have long list of tournaments is when I pre-schedule the tournaments for the coming month, so players who use the "Wanna Duel" link for local tournments can find us.
Another tip is to include your store name in the Tournament title.
For example, our next tournament is "Stonebridge Games Tues Nite Yu-Gi-Oh! (11/22/08)" not "Tuesday YuGiOh" or "Advanced Format YuGioh". When a player looks at his ranking and play history, it will make more sense and be reminder when he visited your store.
Formerly ZombieMasterBlud
Denver Area Judge
Stonebridge Games Regular
YuGiOh Rules Knowledge: LV 2
WoW Rules Knowledge: LV 1
Player Management: LV 1
Tournament Organization: LV 1