The so called "missing assets" were still referenced in the route map files which Trainz used to rebuild the kuid-table so they would re-appear. The only way to delete missing assets is through the Delete missing assets menu command.
The case I am describing is different from deleting missing assets. If the asset is not placed on the map, and is not in the system, but in the kuid table, then it will be reported as a missing asset by the CM. Deleting it from the table solves this, if I remember right, which I may not..