@pitaj vestacp has several nginx.conf. As I mentioned I edited "site-specific" config in /home/admin/conf/web where vestacp keeps configs for all hosts, inculding ssl and lets encrypt.
Maybe you mean global nginx.conf which is located in /etc/nginx ? I did no changes in it.
Using ubuntu's built in yes command you can force it to answer yes to a particular command, so I edited the start.sh script and forced it to answer yes to anything with prompts, would be great for this to be added to the official scripts if possible!