If you save the change to the package, the package is permanently upgraded. When you open the package file in SQL Server Data Tools (SSDT), the package is temporarily upgraded to the format that SQL Server 2012 Integration Services (SSIS) uses.
When you add the package to an existing project, the package is permanently upgraded to the format that SQL Server 2012 Integration Services (SSIS) uses. You can load and run packages that were developed in SQL Server 2005 Integration Services (SSIS) and SQL Server 2008 Integration Services (SSIS), in the SQL Server 2012 version of SQL Server Data Tools (SSDT).