Actually web server logs are stored in /var/www/vhosts/system/example.tld/logs/
.
Log files in /var/www/vhosts/example.tld/logs/
it's not a files but hardlinks to files in /var/www/vhosts/system/example.tld/logs/
. Pay attention for same inode number 261064:
# ls -lia /var/www/vhosts/example.tld/logs/error_log
261064 -rw-r--r--. 2 root root 2432 Jun 8 18:26 /var/www/vhosts/example.tld/logs/error_log
# ls -lia /var/www/vhosts/system/example.tld/logs/error_log
261064 -rw-r--r--. 2 root root 2432 Jun 8 18:26 /var/www/vhosts/system/example.tld/logs/error_log
when I've remove this file I've remove hardlink:
# rm /var/www/vhosts/example.tld/logs/error_log
rm: remove regular file `/var/www/vhosts/example.tld/logs/error_log'? y
# ls -lia /var/www/vhosts/system/example.tld/logs/error_log
261064 -rw-r--r--. 1 root root 2432 Jun 8 18:26 /var/www/vhosts/system/example.tld/logs/error_log
When I've create it again it will has own inode number(276777):
# touch /var/www/vhosts/example.tld/logs/error_log
# ls -lia /var/www/vhosts/example.tld/logs/error_log
276777 -rw-r--r--. 1 root root 0 Jun 8 18:33 /var/www/vhosts/example.tld/logs/error_log
So to solve you issue you just need to remove file you have created and create hardlink to file in system/log:
# rm /var/www/vhosts/example.tld/logs/error_log
# ln /var/www/vhosts/system/example.tld/logs/error_log /var/www/vhosts/example.tld/logs/error_log
# ls -lia /var/www/vhosts/example.tld/logs/error_log
261064 -rw-r--r--. 2 root root 2432 Jun 8 18:33 /var/www/vhosts/example.tld/logs/error_log