Thanks for your message. This is happening because the old shortcode system has been updated and it doesn’t working anymore from the version of 4.5. You need to recreate shortcode and confgure them. You will be pleased to know that now the shortcode system is more easier than it was. You can save and control all the configuration by post type.
Thanks
Currently this can’t be done in our plugin. We’re trying to add this feature. I hope very soon this template overriding feature will be available for all.