If after an account restoration or any other action you don't see a domain on a "Custom HTTPD Configurations" page in Directadmin, and you are still sure that domain exists at an user level on a server, then there is a quick way to get it fixed.
Directadmin reads the file: /etc/virtual/domainowners in order to get a list of domains hosted on a server. So if for any reason the file is missing a domain which is hosted on the server, the domain won't be displayed on the "Custom HTTPD Configurations" page in Directadmin. Thus to get it fixed you simply need to add the missing domain into the file. Be careful to use a correct format:
Where instead of example.com you should specify your real domain name which is missing on the page, and instead of userbob you should use a real username of domain's owner.
echo "example.com: userbob" >> /etc/virtual/domainowners
And now reload and check the page in a browser. You should see the domain on the page.
P.S. IMPORTANT! The file should have a final empty line at the very bottom.