For security reasons, it is best not to let your production environment simply grow from your pilot project. After you assemble a complete record of your final site hierarchy design considerations and are ready to proceed to final site design, you should dismantle your pilot project.
The best way to prevent potential security problems is to completely reformat and prepare each computer for production from a clean state. Remove and reinstall SMS, SQL Server, and Windows NT to ensure that your production databases, security settings, and site hierarchy can be created without any configurations or data left over from your pilot project.