EPUB sync back behavior, what to expect?

What would be really nice would be to have some documentation on what behaviors to expect rather than having to discover things by experiment. For example, I am currently trying to figure out what is supposed to happen with ePub documents downloaded directly from iTunes U to an iPad or other iOS device.
Here's what I have observed. I have a collection (http://itunes.apple.com/WebObjects/MZStore.woa/wa/viewPodcast?id=421137560) that contains an ePub document titled "Raskin Invents First Mac." I use an iPad 1 under iOS 4.3.1 and the iTunes.app on it to directly download this ePub document to the iPad from iTunes U.
The ePub document appears in the iBooks.app and is fully functional there. Connecting that iPad with the Mac to which it is synced and clicking the Sync button, I then look at the Devices > Books and see that the ePub is listed twice despite the fact that only one copy of it can be found on the iBooks bookshelf. Thus, the weirdness begins.
Looking next at Library > Books, I fail to find that ePub document at all despite repeated Syncs. I know that when I "purchase" an ePub from the iBookstore that syncing invokes a dialog asking me whether I want the item synced back from the iPad to the computer and explaining that if I decline to do so that the item will be deleted from the iPad. That doesn't happen when the ePub document comes from iTunes U. To summarize, downloading free ePubs from the iBookstore entails the opportunity to sync back to the "home" computer whereas downloading free ePubs from iTunes U does not offer that choice nor does it do that automatically.
I'm not a UI or HIG expert but consistency seems to be a basic requirement for effective interfaces with digital devices. What I've observed really can't be characterized as consistent.
Surely, this behavior cannot be intentional. It must be a bug, right?

Check the dates that those folders were actually backed up. Originally Time Machine backed up my "Downloads" folder, at some point later I excluded the "Downloads" folder. If I look at Time Machine it still shows that folder, but it hasn't been backed up for weeks.

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