Hi rikyulin,
Sorry to hear that, we have updated a bunch of servers and sites without any problem.
We have made changes in the nginx conf, but nothing significant to have these issues. The only thing that comes to my mind is that you should try this:
In /etc/nginx/common/php.conf
# Change this line:
try_files $uri $uri/ /index.php?$args $uri =404;
# Remove the 404 part:
try_files $uri $uri/ /index.php?$args;
Also, check your logs and look what you can find.
sudo log -php
sudo log domain.com -error
sudo log -error
Regards.