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I guess I'm dense but don't we all keep backups of our libraries?
If you like calibre for it's organization and love your own file structure for day to day use why not use calibre for your organization and backup on another drive. It works very well with the library on my external usb hard drive.
I was very resistant to the file structure thing until I started using epub as the main reading format after purchasing a tablet.
Once I got used to the various methods of exporting it made me rethink my problems. I had been resistant because my device didn't read metadata and the only way I could read a series in order was to have the series name/number in the title.
When I saw that I can do this so easily on export it removed the last of my resistance to using calibre for maintaining my entire library in all formats, not just epub.
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