What I did (TS2009, but I think it will work for TS2006) is in CMP, create a back-up of the asset you want to remove. Then delete the asset from the database. This will only work for assets not built in, as you cannot delete built-in.
Once the asset is deleted in CMP, go back into TS, and use the "Delete missing assets" function.
I do not think that just disabling the asset in CMP will do anything. Disabling only makes the asset no longer available in the Surveyor menu, but does not remove it from the route.