This occurs because Blackbaud NetCommunity locally references images, documents, stylesheets, etc. If this issue occurs, it is due to how the second website is being staged, and not an issue with Blackbaud NetCommunity. If the environment is staged in such a way that the second version of the site cannot resolve the local references to images, documents, and stylesheets, you will receive the 'error: 404 file not found' message where those components are referenced throughout the site.
Please contact your Network Administrator to determine a manner of staging the second site in such a way that the second site can resolve the local references to these components.
This would not occur in the Blackbaud Hosting Services Environment, as we stage multiple domains/sites in such a manner that they can resolve the local references to these components.