There is really no need to copy the themes to use them or change them. You can always extend them. In fact, if you copy the reindeer theme, you will have two themes in your classpath and they might conflict. Check out the Book of Vaadin on how to
create and use themes.
Whether you copy the files or not, you should use a theme with a different name to avoid conflicts, so the path would be VAADIN/themes//styles.css and using setStyle() for the application. All the other files would then also be in that same directory, just like they are in reindeer directory.
Edit: Seems like you already figured it out while I was writing this, never mind