See, that's why I use drag and drop. Sonys software and calibre (and other programs alike) are only databases. So they have to move/copy your file to a specific location to be able to find it again (but maybe not the user himself as he could mess things up this way).
I drag and drop my files. After that, I open the Sony library and organize my books in collections right on the reader. No need for a sync.
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