If you're putting your files in separate versions in wyBuild (as described in the walkthrough: https://wyday.com/wybuild/help/walkthrough.php ), and the patches are installing correctly (i.e. the rollback patch is not being installed: https://wyday.com/wybuild/help/faq.php#catch-all ), then everything should work correctly and files and folders that are not "there" anymore will be removed.