You can delete any 3D objects by right-clicking on it > Edit > Deleted Selected Objects. This will initiate a pop-up asking if you want to simply delete the 3D Object or the Resources with it.
If you Synchronize the same model in the future, all the objects delete within SYNCHRO Pro will be loaded again. To avoid this, you can either delete the unwanted objects in the original modeling software or create 3D filters within SYNCHRO Pro. These filters can be used to select all the objects within it and delete in a single click, or simply unload/hide it.