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After playing with KSM and fmon a little bit, I can be sure that the culprit must be something between Calibre and fmon. My previous statement of the usability of KSM might due to strong luck.
As the remuneration of my water proof function, I got this conclusion:
The database corruption occur if and only if any script in $mount_root/.kobo/fmon/ is executed And using calibre for file moving.
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