According to our development team, these SWFs may appear in case Internet Explorer 8 is used if you’re using a version before 16.1. WIth 16.1 we released HTML5 media players which don’t produce SWFs. Deleting them shouldn’t be an issue.
I believe in one of the next upcoming releases we should be including a publishing option for HTML only like Lectora Online currently has. The feature is described on the Lectora Online section of the website as such: “Select the “HTML5 Only (no Flash included)” publish option to exclude the Flash media player (swf) files from the published content that are used for fallback on older browsers. This will ensure you can successfully import the course into any LMS that disables the use of Flash.” So no more deleting if the option is turned on 🙂