In​‍​‌‍​‍‌​‍​‌‍​‍‌ intricate hosting environments, minor configuration scripts are still very important for system integrity and account accessibility. The cPanel updateuserdomains is one such vital instrument, which is the script that links domains with the right user accounts. A bug named CPANEL-49179 caused this to stop happening, so that the user accounts that were already there and had reserved usernames became invisible to WHM and any other management tools.

The problem caused the administrators to be terribly confused because it looked like the accounts that were affected had disappeared; however, the data of these accounts was still there on the server. cPanel didn’t waste time looking into the issue and came up with a solution to not only make those affected accounts visible again but also fix the underlying logic error for the handling of reserved names ‌ ‍ ​‍​‌‍​‍‌​‍​‌‍​‍‌names.

Technical recap

  • The updateuserdomains script builds/updates /etc/userdomains and other mappings from the per-account metadata in /var/cpanel/users. A change in reserved-username handling caused the script to treat preexisting accounts whose usernames now match newly reserved names as invalid and omit them from the mappings. The accounts’ files and data remained on disk, but they were no longer visible in WHM/account listings.
  • Reserved usernames exist to prevent collisions with system/service accounts. The protection logic should only apply to new account creation; it must not hide accounts that existed before the restriction was introduced. The bug caused exactly that undesirable behavior.

How to tell if you were affected

  1. Accounts missing from WHM or /etc/userdomains while their user directories still exist under /var/cpanel/users or /home/<username>.
  2. Errors or odd behavior when running /usr/local/cpanel/scripts/updateuserdomains (e.g., accounts not appearing in its output).
  3. Related support posts and changelogs mentioning CPANEL-49179 and the fix (indicates a published issue affecting multiple hosts).

A quick SSH check you can do as root:

  • ls /var/cpanel/users | grep -i <username>  confirms the account file exists.
  • grep ^<username>: /etc/userdomains shows if it’s listed in /etc/userdomains.
     If the account file exists but /etc/userdomains lacks the mapping, the account was likely affected.

What cPanel changed 

cPanel released a patch that prevents updateuserdomains from hiding preexisting users when their usernames match reserved names. The patch was included in the public changelogs for the released builds (see the 130/126/118/110 change logs listing CPANEL-49179). Once the updated cPanel build is installed, affected accounts should become visible again without manual re-creation. 

Immediate remediation steps

  1. Backup first. Take a snapshot or at least backup /var/cpanel/users and /etc/userdomains before changes.
  2. Confirm presence on disk: check /var/cpanel/users/<username> and /home/<username> (or the expected homedir). If the files are present, the data is intact.

Update cPanel to a version that includes the patch. As root, run:
 /usr/local/cpanel/scripts/upcp

  1.  Updating ensures the permanent fix is applied rather than relying on manual workarounds.

Re-run updateuserdomains to rebuild mappings after the update:
 /usr/local/cpanel/scripts/updateuserdomains

  1.  Then confirm the accounts reappear in /etc/userdomains and WHM.
  2. If immediate visibility is required and an update is not possible, you can, with caution, manually re-add the domain mapping in /etc/userdomains using the format domain.com: username. This is a short, risky workaround and should only be used if you fully understand the implications—prefer the official update when possible.

Verification after remediation

  • After upgrading and running the script, verify:
    • grep ^<username>: /etc/userdomains returns the domain mapping.
    • The account is visible in WHM – List Accounts.
    • Websites and services (email, FTP, cron jobs) tied to that account function normally.
  • Check logs for any warnings or errors related to username validation or updateuserdomains: /usr/local/cpanel/logs/error_log and system messages.

Prevention & best practices

  • Keep cPanel updated: The changelogs show the fix was shipped in recent releases; regular updates mitigate regressions and security issues.
  • Avoid creating accounts using reserved usernames going forward:  Use the cPanel-provided method to list reserved usernames if you need to validate names programmatically.
  • Implement a change control: Document and schedule upgrades, and monitor logs after updates for unexpected behavior.
  • Maintain backups and snapshots: Maintain backups and snapshots of /var/cpanel/users and account homedirs so you can recover quickly if something unexpected happens.

If the update doesn’t restore accounts

  • Collect evidence: copies of /var/cpanel/users/<username>, /etc/userdomains before/after, and relevant cPanel logs, then open a cPanel support ticket (reference CPANEL-49179) or consult a qualified administrator. The cPanel support articles and change logs indicate the case and the fix path.

Conclusion

CPANEL-49179​‍​‌‍​‍‌​‍​‌‍​‍‌ is an important signal that even though the username validation logic is a safety measure, it should be handled cautiously in such a way that it does not hide legitimate data from the past. The right permanent solution is the vendor patch; keep away from ad-hoc workarounds if it is not necessary, and if you have made a note of it.

ServerAdminz are able to take care of patch management, check the trustworthiness of accounts after the system is updated, and carry out the monitoring and backup processes that will lessen the operational ​‍​‌‍​‍‌​‍​‌‍​‍‌risk.

If you need any support with cPanel maintenance, account recovery, or server performance optimization, contact ServerAdminz for expert assistance.