Issue with WHMCS Updates on DirectAdmin Overwriting/Skipping Files

falazvahid

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Joined
Feb 14, 2026
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Hello,


I’m experiencing an issue with updating WHMCS on DirectAdmin that doesn’t happen on cPanel.


When I try to update WHMCS by moving the update files into public_html, DirectAdmin behaves differently than expected:


  1. Some directories (e.g., whmcs841/admin or whmcs841/install) show errors like:


<span><span>statx (root=/home/username) domains/example.com/public_html/whmcs841/admin: no such file or directory<br>statx (root=/home/username) domains/example.com/public_html/whmcs841/install: no such file or directory<br></span></span>

  1. Most files show messages like:



<span><span><span>File</span></span><span> domains/example.com/public_html/aff.php already exists, file skipped<br></span><span><span>File</span></span><span> domains/example.com/public_html/clientarea.php already exists, file skipped<br></span><span><span>File</span></span><span> domains/example.com/public_html/templates already exists, file skipped<br></span></span>

…meaning that DirectAdmin skips existing files instead of merging or overwriting them, which causes the update to fail or leaves the installation in an inconsistent state.


The main problem is that I have a custom WHMCS template and some customizations, and they risk being overwritten or skipped during the update. On cPanel, this same update works perfectly because the upload/merge process handles existing files safely.


My question:


  • How can I safely update WHMCS on DirectAdmin without losing custom templates or modules?
  • Is there a way to force DirectAdmin to merge and overwrite files like cPanel does?
  • Any recommended workflow for WHMCS updates on DA to avoid this issue?

Thanks in advance for any advice!



 
Get a softaculous license for around $1 a month, and it will handle all your updates and installs properly. It's also safe to use this to install WHMCS and then remove Softaculous if you don't need it after, but in my experience its so beneficial to pay that $1 to keep the license as it handles all installs, backups and removals effortlessly leaving you time to do the things that matter for your business.

Updating WHMCS can also be done once it's installed from the admin panel in WHMC once you've set up the temp directories.


Regarding custom templates, keep a backup before you update and follow WHMCS guidelines on custom templates in custom folders so they don't get overwritten.

 
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