Super late to the conversation, but I download my Audible books into iTunes, and then I set up a playlist "plays is 0" so that only unlistened to books are loaded onto my iPhone.
I use the Audible app to actually listen to the books -- you can choose from "Cloud" (Audible cloud), "Device" (downloaded from Audible and on your device) or "iTunes" (Audible books in iTunes) and I always choose iTunes. When I sync, the books I've already listened to are automatically removed from my phone and I don't have so much clutter to page through.
I don't use Whispersync so I don't know how that is affected.
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