A Amazon publicou recentemente um press release anunciando que agora você pode alterar o VPC para instâncias de RDS existentes:
You can now easily change the Amazon Virtual Private Cloud (Amazon VPC) used by your Amazon RDS DB instance. You can specify a new VPC for an existing DB instance deployed in Single-AZ configuration by using the Amazon RDS Management Console, the Amazon RDS API, or the AWS Command Line Tools. In addition, if you are running your DB instance on the EC2-Classic environment, you can switch to the EC2-VPC environment by modifying your existing DB instance. If your AWS account was created before 2013-12-04, you are potentially running RDS on the EC2-Classic environment.
This feature is available for all regions supported by Amazon RDS, and is available for all supported versions of MySQL, MariaDB, Microsoft SQL Server, Oracle, and PostgreSQL.
Note that this feature is only supported for DB instances running in Single-AZ deployment. If you would like to change the VPC environment of a DB instance in a Multi-AZ deployment, you can temporarily modify your instance to a Single-AZ deployment and then re-enable Multi-AZ once you have changed to the EC2-VPC environment.