Please, take a look at this old post about the Dynamic Prototype feature to make sure you use it in the way it was initially designed:
Our build system builds only linked resources. If you never link the resource anywhere, it will not be built. A ‘linked resource’ in this case means being specified in a factory or in some other place specific to that resource. It’s not enough to be in the project folder.
If you want to have a few levels in your game, just create a few collection proxies (or collection factories).