One of the features of MapifyPro is that you can completely delete the plugin and reinstall it and your data will be preserved.
This ensures that your data is safe! This is because maps and map locations are stored as native WordPress posts (which are hidden from the user).
Unfortunately it doesn't really work well for you in this case if you want to delete all of your map locations! The only option would be to perform a bulk delete of your map locations page by page. You will also need to delete it from the trash.