Ashley,
This is intention as overlaying two almost identical projects can lead to numerous errors that people would then come back to the forums with things like “I’m changing my files and they aren’t getting deployed, Tomcat keeps loading the old copy!”, but the real issue is that since the deployment is a mish-mosh of the two projects, there is likely some loading of wrong resources going on there.
We make it mandatory to erase the old project to somewhat forcefully help people to avoid conflicts and weird situations. You can of course avoid this by changing the two separate contexts to something like /myapp1 and /myapp2… can you explain your use case such that you need both projects to have exactly the same context *and* you need them to overlap eachother?