It looks like apt is trying to connect via IPv6 but for some reason can't (but it isn't being blocked, the packets just disappear). Check that the computer you are trying to upgrade actually has internet connectivity with IPv6. If you only have an IPv4 connection to the world, then according to this question/answer you can force apt to use IPv4 with the -o Acquire::ForceIPv4=true
option:
apt-get -o Acquire::ForceIPv4=true update
or to force it permanently, create a file with a name like /etc/apt/apt.conf.d/99force-ipv4
containing this line:
Acquire::ForceIPv4 "true";