Re eBooks added to an iPad, what determines whether it will be sync'd back to iTunes?

I'm trying to figure out the rules of the road for back-syncing from an iOS device such as an iPad and the iTunes.app on a Mac or Win desktop machine.  In particular, I  am interested in ePub-based eBooks gotten from sources other than the iBookstore.  There are a number of possibilities:
o Sideloading to the iOS device via iTunes.app with "Manually manage music and videos" selected.  With this setting, one can drag and drop an eBook onto the device in the Devices listing in iTunes.app.  The ePub files transferred to an iOS device this way do not seem to be sync'd back to the iTunes.app on MacOS X regardless of the status of the "Manually manage ..." setting.  The Calibre eBook library management app has a similar direct transfer function.
o Using Safari for iOS, one can tap on a hyperlink to an eBook on a properly configured HTTP server (proper MIME Type declared for the .epub suffix) and be prompted to hand it off to iBooks or another app that iOS thinks might be able to handle it.  The ePub files transferred to an iOS device this way appear to get synched back to iTunes.app on the MacOS X desktop if "Manually manage ..." is not selected.
o I don't believe that the iBooks.app supports OPDS catalogs so that's not a point of entry.  Anyone know otherwise?  However, there is an iOS app called "eBook Search" that does and it will hand off ePub documents located in OPDS catalogs to iBooks using the same interface as Safari on iOS.
o An iTunes U public site via the Podcasts.app or an iTunes U Course via the iTunes U.app will download ePub books and hand them off to iBooks. 
There are probably more ways than I have discovered to get ePub documents into the iBooks.app on iOS without involving either the iBookstore or  the iTunes.app.  So the question is, "What do I tell my students who are on a scavenger hunt for free, unencumbered (no DRM) ePub documents?  They will want to know what will happen after they get them on their iOS devices?  Under what circumstances will they be kept, erased, copied back to iTunes.app (or iCloud) and so on?
I have not yet found any Apple documentation on this important question.  Any leads will be appreciated.

Recovery Mode
1. Disconnect the USB cable from the device, but leave the other end of the cable connected to your computer's USB port.
2. Turn off the device: Press and hold the Sleep/Wake button for a few seconds until the red slider appears, then slide the slider. Wait for the device to turn off.
3.While pressing and holding the Home button, reconnect the USB cable to the device. The device should turn on.
4. Continue holding the Home button until you see the "Connect to iTunes" screen. When this screen appears, release the Home button. iTunes should alert you that it has detected a device in recovery mode. Click OK, and then click Restore to restore the device.
Note: Data will be lost.

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