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I had that concern too. I found calibre so much better than Sony's library software, so I stayed away from purchased books as long as possible.
I found by trial and error, (and some help through this forum), that the Sony software is necessary just to get your ADE ID transferred to the reader - without it installed ADE did not detect my reader - but after that it can be uninstalled.
ADE works quite happily alongside calibre with any ePubs you care to throw at it, and it does so without touching your reader or your calibre library.
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