Commonly, EOS Windows Server applications also have EOS SQL Server databases. The recommended approach is to upgrade the database to a modern version as SQL Server database upgrades are handled outside the EMP process. You can also modernize to AWS purpose-built, cloud-native databases such as Aurora. You can learn more about those options here.
If you find that a specific SQL Server database cannot be upgraded or an upgrade breaks application functionality (even in compatibility mode) then you can fall back to creating an EMP package for the legacy version of SQL which can then be deployed onto a modern EC2 Windows instance.
For instance, this EMP demo video showcases how SQL Server 2000 can be packaged and deployed to a Windows Server 2019 instance in AWS.