I don't think you need to flash your eMMC, rootfs should be sufficient
https://wiki.maemo.org/Updating_the_tablet_firmware

Some possible causes of dpkg db corruptions could be:
* undervolting lead to data corruption
* dpkg db was moved to /home and the new MMC bouncing damaged it (unlikely, this feature is default on most Linux distros)
* crash+reboot during dpkg operation