If you need to enable or disable DKIM for a specific domain or domains on your server without making a change to all domains on the server, you can use the WHMAPI to quickly complete this task.
From the command line, you can use the following commands.
Enable DKIM for the domain(s):
whmapi1 enable_dkim domain=example.com domain=anotherexample.com
Disable DKIM for the domain(s):
whmapi1 disable_dkim domain=example.com domain=anotherexample.com
For further details on the API call please see the documentation: