If you want to remove a map, you must remove it from the map manager. You must also remove it from the UI.

For Lightspeed maps, the easiest way to make sure that you perform all necessary steps is to use the API utility methods.

TLcyLspMapAddOn mapAddOn = aLucyEnv.retrieveAddOnByClass(TLcyLspMapAddOn.class);
TLcyLspMapBackEnd mapBackEnd = mapAddOn.getMapBackEnd();

//This method removes the map from the UI and the map manager.