the kobo uses "lazy umount" before USB export. unfortunately the way lazy umount works is that the filesystem "disappears" but in reality nothing is umounted at all if the filesystem is busy. so kobo ends up exporting the filesystem in dirty state.
in original unpatched kobo firmware this used to be the case when connecting it to USB out of a kepub book. but I haven't tested this condition recently so I don't know if this is still the case. if you modded the device it's possible for those mods/addons to block umount as well.
I tried to make a debug utlity for this condition at some point
https://www.mobileread.com/forums/sh...d.php?t=263674 but it probably won't work anymore in current firmware, haven't updated in ages