I stopped using FDLite a while ago in favour of using the routes download available at
http://groups.yahoo.com/group/PP-logs-and-routes/If you've got specific examples of missing routes I'm happy to check if these are included in that download. Today's download includes 859 KLM routes, 572 EIN routes, and 1155 BAW routes.
If you decide to use the database from Yahoo groups, this query generates what you need to import into Radabox:
SELECT DISTINCT
FlightRoute.flight AS FN,
substr(FlightRoute.route,1,4) AS NO,
substr(FlightRoute.route,length(FlightRoute.route)-3,4) AS ND,
"" AS NV,
substr(date('now'),1,4) || substr(date('now'),6,2) || substr(date('now'),9,2) || "090000" AS CH
FROM
FlightRoute
ORDER BY
FN