If you notice that an account is missing from your WHM instance and you’ve already attempted to fix this by running /scripts/rebuildcpusers (you have tried this, correct?), then the issue lies in the /etc/trueuserdomains file. To correct this you will need to manually edit this file (using VI, Nano, Pico) and add the domain and the user account assigned to that domain. For example;
My user is Myuser(it really isn’t) and the domain is Mywebsite.com. I would edit this in the file by added it as such:
Mywebsite.com: Myuser
Once this is done, save the file and restart cpanel. Once you access WHM, the directory will appear again.
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