Hi,
Currently one of our server having weird problem after autoupdate.
The files inside /scripts/ become 0kb in size.
[root@main scripts]# ls -la
total 12
drwxr-xr-x 2 root root 4096 Sep 3 03:38 .
drwxr-xr-x 7 root root 4096 Aug 2 06:59 ..
-rwxr-xr-x 1 root root 0 Dec 1 2016 add_alert
-rwxr-xr-x 1 root root 0 Jan 7 2019 apache_mpm_calculator
-rwxr-xr-x 1 root root 0 May 13 16:44 apache_server-status
-rwxr-xr-x 1 root root 0 Sep 17 2018 autossl_fix_tmp_path
-rwxr-xr-x 1 root root 0 Dec 18 2018 autossl_generate_apache_conf
-rwxr-xr-x 1 root root 0 Aug 18 09:12 bandwidth_run
-rwxr-xr-x 1 root root 0 Mar 13 2018 check_api
-rwxr-xr-x 1 root root 0 Apr 5 2017 checkdb
-rwxr-xr-x 1 root root 0 Nov 17 2016 check_postqueue
-rwxr-xr-x 1 root root 0 Apr 2 2018 clamd_fix_100_cpu_usage
-rwxr-xr-x 1 root root 0 Aug 23 06:45 cpanel_addhandlers
-rwxr-xr-x 1 root root 0 Aug 16 16:52 cwp_api
-rwxr-xr-x 1 root root 0 Jun 28 2015 cwp_bruteforce_protection
-rwxr-xr-x 1 root root 0 Jun 28 2015 cwp_monitor
-rwxr-xr-x 1 root root 0 Aug 8 06:20 cwpsrv_rebuild_user_conf
-rwxr-xr-x 1 root root 0 Mar 22 2017 cwp_version
-rwxr-xr-x 1 root root 0 Oct 28 2016 disk_check
-rwxr-xr-x 1 root root 0 Jul 10 08:12 dns_sync_slave2
-rwxr-xr-x 1 root root 0 May 26 2018 dso_handler_remove
-rwxr-xr-x 1 root root 0 Nov 14 2016 freshclam
-rwxr-xr-x 1 root root 0 Aug 28 06:15 generate_hostname_ssl
-rwxr-xr-x 1 root root 0 Aug 28 06:36 image_rebuild_server_config
-rwxr-xr-x 1 root root 0 Sep 28 2018 install_acme
-rwxr-xr-x 1 root root 0 Aug 28 06:31 install_api
-rwxr-xr-x 1 root root 0 Jun 28 2015 install_imagick
-rwxr-xr-x 1 root root 0 Jun 28 2015 install_maldet
-rwxr-xr-x 1 root root 0 Apr 21 2016 install_net2ftp
-rwxr-xr-x 1 root root 0 Jun 3 16:29 install_netdata
-rwxr-xr-x 1 root root 0 Aug 28 05:58 install_pure-ftpd_tls
It is also same in the folder /usr/local/cwpsrv/htdocs/resources/admin/include/
[root@main include]# ls -la
total 92
drwxr-xr-x 11 root root 4096 Sep 3 03:38 .
drwxr-xr-x 7 root root 4096 Aug 2 06:59 ..
-rw------- 1 root root 87 Aug 13 02:34 3rdparty.php
drwxr-xr-x 4 root root 4096 Sep 3 03:38 ai_robot
-rw-r--r-- 1 root root 0 May 17 08:26 alertandautorenewssl.php
drwxr-xr-x 2 root root 4096 Sep 3 03:38 api
-rw------- 1 root root 0 Aug 16 17:48 api.php
-rw-rw-r-- 1 root root 0 Nov 9 2018 autossl.php
-rw-r--r-- 1 root root 0 Oct 12 2018 autoupdate_3rdparty.php
drwxr-xr-x 2 root root 4096 Sep 3 03:38 cgi
-rw------- 1 root root 0 May 7 05:20 chk.php
drwxr-xr-x 2 root root 4096 Sep 3 03:38 common
drwxr-xr-x 2 root root 4096 Sep 3 03:38 config
-rw-r--r-- 1 root root 870 Aug 5 00:04 configserver.php
-rw-r--r-- 1 root root 0 Aug 30 11:07 cron_autossl_all_domains.php
-rw-r--r-- 1 root root 0 May 17 05:08 cron_autossl_renew_all_domains.php
-rw------- 1 root root 0 Jun 23 02:14 cron_backup.php
-rw-r--r-- 1 root root 0 Aug 31 22:48 cron_migration_cpanel.php
-rw-r--r-- 1 root root 0 Aug 29 07:01 cron_migration_cpanelv2.php
-rw-r--r-- 1 root root 0 May 17 05:05 cron_newbackup.php
-rw-r--r-- 1 root root 0 May 17 05:07 cron_notificate_user.php
-rw------- 1 root root 26177 Sep 3 16:57 cron.php
-rw-r--r-- 1 root root 0 Apr 2 2018 cron_rbl.php
-rw-r--r-- 1 root root 0 Aug 31 22:50 cron_restore_acc_cpanel.php
-rw-r--r-- 1 root root 0 May 18 22:57 cron_transfer_accounts.php
-rw------- 1 root root 345 Aug 9 13:13 db_conn.php
-rw------- 1 root root 0 Aug 30 16:40 functions.php
We don't know what cause the problem.