Replace With Prefab functions from the right click menu (ctrl + k | ctrl + shift + k) do not function on vanilla locked assets. They only function if the prefab you are changing to is duplicated into your mod. This leads to a TON of bloat.
Steps to Reproduce
Place down 10 40ft Red Cargo Containers
Randomly select 3 of them in the hierarchy
Right click and select "Replace with Prefab" -> "In World"
Select a different 40ft Cargo Container color
Nothing happens
Steps to Actually Get It To Work
Place down 10 40ft Red Cargo Containers
Duplicate another 40ft cargo container color to your mod
Right click and select "Replace with Prefab" -> "In World"
Select your duplicated cargo container
Successfully swaps the prefab