[Junket]

I edited my earlier reply for clarity. A factory reset would mess up your jailbreak. But the hotfix file that you installed should allow you to reinstall the jailbreak without using the serial adapter as long as you don't also allow a firmware update in the process.

As to removing your current books from the Kindle, a factory reset isn't the only way to do that. You could also use the remove item menu or the Amazon account manage your device page (if you let your Kindle talk to Amazon) or by resyncing with an Calibre if Calibre is configured to remove as well as add sync items for instance.

Since it sounds like you side load your books and keep your PW in airplane mode the simplest method is probably to connect your Kindle to your PC and use a file manager to delete the books in the folders there. It might take several restarts before the links to the deleted books on the Kindle home screen update though.