Done :)

Check out http://stackoverflow.com/questions/11426087/nginx-error-conflicting-server-name-ignored 

Yes, everything that isn't server {} goes to GUI. All files in /etc/nginx.custom.d get included into NGINX's root http {} section.

Currently you have to add it manually, but a GUI editor will be added soon.

You can't insert server{} sections into another server{}. Put your snippet into /etc/nginx.custom.d/yourconfig.conf and restart NGINX.

I know, this is the intended behavior. What's the point of having no files in Notepad anyway?

No problem :)

Are you 100% sure that your existing config got completely erased? There's nothing in the fail2ban plugin that automatically touches the existing configuration at the moment. Only case when files can get overwritten by Ajenti is when configuring Ajenti V, and then there's a warning about that.