Disappearing Dockers on Ubuntu after updates only happens when the kernel is upgraded. While your solution worked this time, it might not the next time given you had just done an update previously. This is the line you want to run specifically after a kernel upgrade.
sudo apt-get -y install linux-image-extra-$(uname -r) aufs-tools
or bundle them with your update with something similar to this:
sudo apt-get update && sudo apt-get upgrade -yy && \
sudo apt-get -y install linux-image-extra-$(uname -r) aufs-tools
Then you do have to reboot unfortunately. It happens on our Ubuntu servers all of the time. Worst case scenario it doesn’t find an update and just jumps past the line. Perhaps not perfect but effective and fast. I hope this helps!