Contrary to popular belief, I am not a mad hacker - I hack when it's safe, more efficient, or the only option. If the officially approved method works easily and reliably enough I always use that.
So, step 1: Find the KUID I want to get rid of in Content Manager, Save it to CDP, then delete it.
2: Open the route in surveyor, click Main menu, Delete Missing Assets, save route.
3: Back to Content Manager, select the route and Check Dependencies, View in Main List. Make sure that KUID is gone, then reinstall it from the CDP if I need it for something else.
Directly hacking the config.txt to remove the KUID means the undesirable asset will no longer be listed as a dependency, but the code for it will still be in one of the files, which could cause other problems.