No, the progress will not be affected if Bluestacks will be uninstalled. The application features Google+ integration which means you have the possibility to save the progress on the cloud storage. If you didn't use the Google+ integration, then the progress will be lost because the files containing the saves will be deleted upon uninstalling Bluestacks. However, during the uninstall phase, Bluestacks allows you to keep the userdata and files. Make sure to choose NO when it asks if you want to delete it. Remove Bluestacks, install it again and the progress should be restored.