When opening the file manager from cpanel the files were not showing up under public_html directory.
The issue in this case was caused because of a wrong group established in public_html directory. I had the directory owner like user:user and I had to change it to user:nobody. After changing the group to nobody the files were showed up again.
UPDATE:
You also should check cpanel error log (/usr/local/cpanel/logs/error_log). In other of my clients I checked the error log and I found this message:
Out of memory!
It seems a cpanel bug, because the server had free memory and after restarting the cpanel service the error was gone.
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