Open the file in basecamp, view the route properties, delete stuff as required. Resave the file.
But 200 is the limit? There's no way to use multiple files?
I can't install basecamp onto this machine, something's wrong with the installer failing to work with remnants of an old install. I'll try at home.
Why have you got 200 waypoints? Are you sure regarding the limit of waypoints?. Is this in a single route? The limit for via points and trackpoints is virtually unlimited AFAIK.
It may be possible if you load the waypoints as a custom POI category.
@hippy started
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Open the file in basecamp, view the route properties, delete stuff as required. Resave the file.