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If you are really worried about long-term accessibility, then just store the books in multiple formats, including a plain text one. But on a practical level, it really doesn't matter much. If we are talking very, very long term storage, then readability of the media is a bigger concern (both the format and the material).
My Calibre library is backuped to my tablet, to one of my e-readers, and to an external drive. I also keep incremental backups in case it gets corrupted and I only notice later (those get synced with an external drive as well).
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