When you first log into the WebHost Manager and run the initial setup wizard, the 0-byte file /etc/.whostmgrft is created. If you remove this file, the wizard will run the next time the root user logs into the WHM.
cPanel simply looks for the existence of this file, so it can be empty. To restore the file and prevent the initial setup wizard from being run, touch it:
# ls -alh /etc/.whostmgrft
-rw-r--r-- 1 root root 0 Feb 1 08:07 /etc/.whostmgrft
# rm -rf /etc/.whostmgrft
# touch /etc/.whostmgrft