i have also problems with the update of my system. if apt-get runs over three days and something crashed or power fail, the sd card was damaged and no more usable.
since this day, i have installed the system on this pi with iscsi and use an image on the harddisk of my server. i can update this without damage the sd card, because apt get write many many to the same position on the card on update. on the iscsi-image it makes no differencs if a sector is written one million a time or less.
after update this system, i can copy the update with rsync on any other pi.