Hi Nick, as far as I can tell inactive sidebars are sidebars that previously existed, and had widgets in them, but then something got rid of them in the code (change a theme maybe?) but the database options table still has info about them.
My recommendation is to make a backup copy of the site and use a database tool like phpMyAdmin to look in the options table for those sidebars. Try deleting them from the options table in your backup and see if you can safely remove them that way.
Thank you for that Topher.
As I used Custom Sidebars to generate the sidebar originally, it appears it was located under wp_options as widget_customsidebarempty or something similar to this; the string data in the table too is quite interesting – I always enjoy sifting around inside phpMyAdmin!
Cheers.