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Best check the entire filesystem on the card for errors.
Cybook software is embedded Linux. When such Linux finds any problem on filesystem, during normal operation, it puts the entire filesystem in read-only mode, for safety. It might not tell you that, it will continue operating normally, but from that moment on, until you fix the filesystem, it won't write anything into the files that remember bookmarks and your current position in book. So it won't be remembered.
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