If you get this message from your QNAP:

The file system is not clean. It is suggested that you run "check disk"

and after you start a disk check and you end up with message like this:

[Mirror Disk Volume: Drive 1 2 3 4] Examination failed (Cannot unmount disk).

You need to get into SSH and execute following:

/etc/init.d/services.sh stop
/etc/init.d/opentftp.sh stop
/etc/init.d/Qthttpd.sh stop
umount /dev/md0
e2fsck -f -v -C 0 /dev/md0
mount /dev/md0

After all of above, your QNAP NAS will reboot and everything will get back to normal.