I think we have the option for it in Mission Planner -> Software Tab?
Bump. I can't figure this out either. Where is the Software Tab?
My fix is not the ideal way but it appears to work. I go into the "Full Parameter List", then edit the "FENCE_TOTAL" number and set it to 0, then press "Write Params". The geofence still appears on the mission planner but if you press try to download the current geofence (right click > geofence > download), Mission Planner reports that there is nothing to download. Like I said, you can still see the geofence in Mission Planner, but the autopilot will not recognize it. I was also having issues uploading a new geofence. In order to upload a new one, I go into the "Full Parameter List", then edit the "FENCE_ACTION" and set the value to zero. I then create a new geo-fence. When you press "Upload", the old fence will clear away. Then I go into "FENCE_ACTION" and set it back to 1,2, or 3, depending on which option I want. You can double check that the APM is using the correct fence by going into (right click > geofence > download) and making sure you still see the geo fence you want.