Yeah now that I know what it is doing it isn't so bad, its just that I didn't think about that fact when I was originally importing them into Sony so I have files scattered here and there.
I was thinking though, I should be able to plug my reader into the USB, copy off all the LRF files into one directory, delete them all from the Sony Ebook Library, and then resync, being more careful in the future.
I've been putting all my Sony Reader files in one directory now, I just wish there was some way in Calibre just to save the LRF files out, but apparently there is not.
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