Nginx Several domains keep returning after deletion

• CentOS Version: CentOS 7 64bit ?
• Centmin Mod Version Installed: 123.09beta01
• Nginx Version Installed: 1.13.4
• PHP Version Installed: 7.0.19
• MariaDB MySQL Version Installed: 10.1.26
• When was last time updated Centmin Mod code base ? : Daily
• Persistent Config:
  Code (Text):

  NGXDYNAMIC_NGXPAGESPEED='y'
  NGINX_PAGESPEED='y'
  LETSENCRYPT_DETECT='y'
  ENABLEMOTD_CSFMSG='n'
  ENABLEMOTD_LINKSMSG='n'
  PHP_PGO='y'

Can't seem to figure out what the issue here is. I have a couple domains that are returning after I deleted them. It's not instant; sometimes they come back after a couple hours to maybe a full day. Weird, right?

From what I can tell, they only return to /home/nginx/domains with an empty /public/ folder.
No domain.conf file in /usr/local/nginx/conf/conf.d

One of the domains I removed manually by deleting the domain folder and vhost file followed by restarting nginx.

For the other I used these steps:

Code (Text):

rm -rf /usr/local/nginx/conf/conf.d/domain.com.conf
 rm -rf /usr/local/nginx/conf/conf.d/domain.com.ssl.conf
 rm -rf /usr/local/nginx/conf/ssl/domain.com/domain.com.crt
 rm -rf /usr/local/nginx/conf/ssl/domain.com/domain.com.key
 rm -rf /usr/local/nginx/conf/ssl/domain.com/domain.com.csr
 rm -rf /usr/local/nginx/conf/ssl/domain.com
 rm -rf /home/nginx/domains/domain.com
 service nginx restart

Any idea? This has been going on for months.

Edit: Also thought it could have been something in cron, but I don't think so after looking at it:

Code (Text):

11 */23 * * * /usr/local/src/centminmod/tools/autoprotect.sh 2>/dev/null
0 */4 * * * /usr/bin/cminfo_updater 2>/dev/null
#*/15 * * * * sleep 297s ; wget -O - -q -t 1 http://domain.com/wp-cron.php?doing_wp_cron=1 > /dev/null 2>&1
0 */12 * * * sleep 221s ;/root/tools/wp_updater_domain.com.sh >/dev/null 2>&1
0 0 * * * "/root/.acme.sh"/acme.sh --cron --home "/root/.acme.sh" > /dev/null
15 */3 * * * /root/tools/updatecm.sh 2>/dev/null

---

 

Nothing related in /usr/local/nginx/conf/ssl/
I do see /root/.acme.sh/domain.com for one of my problematic domains. I'll delete this folder and see what happens in the next couple of days

Thanks!

 

Update: Yes, the steps you explained fixed the problem!
Thanks