Is this an iTunes sync bug?

I have an iPhone5 running iOS6.1 with iTunes 11.0.1.12 running on a Windows 7 PC.  Here's the scenario:  I have all my books sync'd up properly between my phone and iTunes.  If I use my phone to download a book I previously purchased (the book icon has the little iCloud symbol on it), it looks like the linkage is broken.  Meaning, deleting or downloading the book on my phone is no longer relected in iTunes and vice versa - checking or unchecking the book in iTunes for sync'ing doesn't result in anything happening on my phone.
Is this a bug, or intentional?  If intentional, what's the reasoning?  Since I would think most of what you do is done through your phone rather than iTunes, it seems this just results in the two getting out of sync.

Yes it is iTunes used to transfer purchases from the device as part of syncing.
The workaround is from the top menu (Ctrl B to turn it on in Windows)
File > Devices > Transfer Purchases from this phone

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    1.  We have an iPhone with a bunch of purchased songs on it and was at one point working with another iTunes library.
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    Rob A. wrote:
    tt2,
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    tt2

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    Myzin wrote:
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