Simple — just delete the file and reload nginx:
rm /var/www/yourwebsite.gr/nginx/limits-root-context.conf
nginx -t && gp ngx reload
And remove the zone definition from limits.conf:
nano /etc/nginx/common/limits.conf
Remove this line:
limit_req_zone $binary_remote_addr zone=sss_search:10m rate=5r/s;
Then sync it to the custom copy:
cp /etc/nginx/common/limits.conf /etc/nginx/common/_custom/limits.conf
nginx -t && gp ngx reload
That’s it — clean removal with no trace left behind.