Hmm - I guess one thing to try would be to reflash with the latest PRSCustomizer or Universal Flasher (which is what the PRSCustomizer builds on) as there's no generic issue with USB. Another would be to try the "Format internal memory" (Settings/Advanced) after saving anything on it you want.
As an aside, if Calibre can copy to it, can you copy books to it via your OS (e.g. Windows) in which case, you might be able to just copy the purchased books across 'manually' although this'll only work if you've previously registered your Reader to your Sony Connect account.
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