iBooks is dangerous - Geniuses at apple store are clueless or lie

It is extremely dangerous to use iBooks to manage any content not purchased from Apple. Making it easy to open and "save" in iBooks a PDF downloaded to an iPad is an invitation to disaster. Backing up your iPad will not do what you might think. Who knows what syncing through iTunes will do.

To add insult to injury, it is a total waste of time to ask for help at the Genius Bar at an Apple Store. They either have no clue about the dangers that iBooks poses or they lie about it.

Does anyone know of a way to actually backup, export, transfer, or otherwise protect a large number of PDFs that were downloaded to an iPad and "saved" in iBooks?