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Most ereaders are based on Linux, and so can be a bit fussy about the filesystem type on the SD card. They mostly require some type of FAT filesystem. It's best to let the ereader format the card before use so that it gets a fully compatible filesystem on it. In this case, you don't want to erase the contents on the backup card, so it would be best to format some other card in the ereader, and then copy the contents from the backup to the formatted card via a PC.
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