If you have the original files installed by an MSI, I think you can do it by using the same Upgrade code.
However, the best solution, assuming you have the original installer as a project, is to update the installer project with the new files, build it, and use the tools in the Windows Installer (Platform) SDK and create a patch.
With Windows Installer installs, you don't just want to overwrite files, you want to manage them according to component rules, and the systems they have provided to upgrade or manage patching.