Introduction
Sometimes you need to automatically update the MX entries for all domains on the server. cPanel has the /usr/local/cpanel/scripts/checkalldomainsmxs script that will attempt to determine if a domain's mail is supposed to be handled locally or remotely.
Procedure
Before running this script, make a backup of these files:
/etc/localdomains/etc/remotedomains
After these files are backed up run this command:
/usr/local/cpanel/scripts/checkalldomainsmxs --yes
Note: As this script affects all domains on the server, you must include the --yes flag when you run the script.