There's really two aspects to this:

1) ClusteredDeploymemtRepository.removeDeployment can't use the VirtualFile from ProfileDeployment.getRoot() as an input the the RepositoryClusteringHandler, because that VF is now a special "backup" copy that the handler can't understand. This is the cause of a testsuite failure.

2) AbstractLocalContentManager should mount each of the URIs it monitors in a separate location, so it can scan the original contents even if some children of those URIs are actually copies created by deployers.