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Kobo runs dos-fsck whenever you pull the USB plug. Also possibly on bootup. If the user partition is found to be corrupt it will factory reset. For the system partition, if I remember correctly there isn't even a fsck for ext4 included so it completely relies on journaling to fix things here. You could fsck it while it's connected to your PC. Or include a fsck binary with this mod...
Problems with Calibre are to be expected; Calibre has a certain set of rules it uses to identify devices, it probably doesn't like deviations too much (things also stop working after firmware updates), so... and I don't allow my Calibre to mount stuff anyhow so I can't test for these things either.
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