What I did was completely empty my flights when I started using ANRB 2009, using SQL:
DELETE FROM Flights;
DELETE FROM FlightsOld;
From what I can see, the Flights table holds the latest 2000 flights, and everything else is in the FlightsOld table.
If you want to be more selective about the deletes, then open the table in something like SQLite Maestro, sort by End Time, highlight the ones you want to delete, and hit the Delete key.
Worth taking a backup before you do any of this - beware!!!