How do I clear off all my files?

I need to take my iPod Touch Gen 5 into the Apple Store where they probably will wipe it.
I am trying to clear all my stuff off starting with my photos.
I imported them all into Aperture and checked for them to be deleted which they seemed to do.
My Camera Rolls show empty in Photos on the iPod but when I look at the iPod in iTunes 11.1.2 there are still 1000 photos occupying 1.4Gb.
I'm also concerned about several custom books I have on the iPod but have lost from hard drive. Is there a way to get those back?

I am also getting:
There are purchased items on the iPos "blahblah" that have not been transferred to your iTunes library. You should transfer these items to your iTunes library before updating this iPod.
I have done a manual backup twice. What am I missing?
Peter

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