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The reader actually recognises the books in the root directory. They are actually better there as they are 100% detected whereas in the proper folder if moved with copy and past its only 80 or 90% as for some reason you get a random book not showing up.
The scan and fix does work and its easier than a reformat. The invalid format is caused by the copy operation being incomplete and bits of the files that were being transferred at the time being split across memory sites that aren't allowed.
Calibre is ok but it can share the problem of slowness as the sony and it has no status element and can't be easily interrupted. Ive actually got calibre just for keep organised but Ive been using book designer and have a folder on my desktop that I have all the converted books on and just copy it right into the reader and skip all the ones already present. Seems to work well and if I need to reformat everything is still there.
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