There is an option to remove the unused linenumbers by means of Plant 3D user intesface. To do this, restart Plant 3D and without any of the project drawing opened (this is the necessary condition in Plant 3D 2013, it may be fixed in the latter versions) run the "_AUDITPROJECT" command. The result of this command is shown in the command line (press 'F2' to view the text window) and it generally includes the Tags of the removed linenumbers. If you check the project database and 'P3dLineGroup' table after running the command and see that there are some of the phantom records present, it means that these linenumbers have existing links in the project database (to Parts or Drawings). So there are some objects in the project drawings on these linenumbers. I strongly do not recommend deleting the records manually from the project databases, as this could result in crushing the project.
