As TSwenson said, you can use the Delete missing assets. This is the brutal and quick to the chase method.
Close your route if you have it open and then close Trainz leaving only the Launcher running.
Open up Content Manager.
Search for your route.
Right-click and list dependencies.
This will open a new window that you can sort by name, type, or however else you want. For this, you want to sort by type.
Scroll down the list until you find the asset.
Highlight it, and then click on the Content menu above.
Click on Disable to disable the asset.
Start Trainz again and open your route in Surveyor.
Ignore the missing dependency thing on the icon. Remember you created the missing asset.
Run Delete Missing Assets and then save your route.
Go back into Content Manager, you don't need to exit your route or Trainz this time and re-enable the asset again. You can do this by looking for hidden or disabled assets. Highlight the asset, click on the Content menu and choose enable.
I've done this a few times when I've run into really horrible boggy assets that caused terrible performance after I put them in. It was one of those things that showed up after I put in lots of them and rather than go over the whole route from one end to the other, it was easier to do it this way.