Putt,
Can you tell me what device and Software version you are on? Also, are you speaking of the Filed Flight Plan (under Online Filing), or simply the Active Flight Plan on the Flight Plan page that your are navigating.
If the later, we moved the Clear All into the More Options. Touch More Options and select "Clear All Waypoints". In the next release we have added back a "Clear" to the top right corner of the Flight Plan page... That will clear the plan like the "Clear All" did of old. I hope this helps.