Example

archive.addResource("my-local-resource.xml", "/META-INF/my.xml") // becomes /META-INF/my.xml
archive.addResource("my-local-resource2.xml", "/META-INF") // becomes the file META-INF, the existing Folder META-INF and sub files are deleted

The second line could be a simple typo on the users side, but with no warning or error you have to debug the archive to even figure out what happened.