Bench setup nginx not updating nginx.conf

My server and sites run smoothly before yesterday.
But I don’t know what happened suddenly my nginx.conf is not updating after bench setup nginx.

I created a new site and ran the bench setup nginx and bench setup reload-nginx but the site was not accessible.
After looking at the nginx.conf, the site name was not in the list. Not in server map, not in 80, not in 443, not in 301 server list.
I then manually added the site name to the list, then I could access the site in the web browser.

As experiment, I deleted the nginx.conf from config folder. And ran bench setup nginx. It didn’t create a new nginx.conf file.

Did anyone has similar issue?
What might be the cause of this?
What should I check to find the problem?

Thank you

I’m not a computer expert, so can anyone please respond on this issue?
Thank you