Greetings,
Don't forget to save your changes.

You must press EXEC after any change to the flight plan or the 480 will
not recognize that change.

Very frustrating to find yourself still going to the deleted waypoint,
but you can't see it.

So....
FPL
EDIT
XPND
Turn the Big Knob to select the waypoint
CLR
EXEC

Fly SAFE!
Jedi Nein