To respond to the original question, I use Calibre mostly, but I have also purchased books in the Sony store and downloaded freebies. In some cases, I have added them to the Reader (700) with the Sony software. But mostly I import the books into Calibre and add them from there. (Partly so that I can Tag them to fit my Collections, partly because I vastly prefer Calibre to the Sony program.)
I've never had a problem. But I also never use both programs at the same time.
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