The website will run as it is under the current license. If the one company who owns the license doesn't want them to part with the license as it is then you may have an issue. But until then I'd say leave them on the EMS license and if they want to upgrade to a new version, they will have to either purchase a license or remove the features they are using.
Another option is to create an instance with the same version and hotfix. Export the site from where it is, ensuring you don't have all the EMS features and objects checked. Then import it into the new instance, again ensuring you don't have any EMS features selected. If you do run across issues with EMS features, run the import and if it fails, run the export and exclude those items. It may take a few tries, but this would be the simplest way to get up and running pretty quick.