To disable it via command line, ssh to the server and run this command:

whmapi1 twofactorauth_disable_policy

This turns two-factor auth off. However, it does not delete the current two-factor setups. So before you turn two-factor back on, you need to disable the two-factor code from your account

Log into WHM
Click on Two-Factor Authentication
Click on “Manage My Account”
Click on Remove Two-factor Authentication
This will remove the current two-factor code from the root user, allowing you to setup a new one.