Deleting data from a device

I have been using Basecamp as a way to fine tune waypoints and tracks based on Birds Eye images, custom maps and vector road maps, which can be somewhat layered and mixed while moving the tracks and waypoints. However it's until now that I find out that If I send a waypoint or track to the gps internal memory or the microsd card, then I cannot delete the item I the new place, only If I delete it from the gps track manager or waypoint manager or from the underlying gpx file. Am I wrong or is this actually a Basecamp limitation?