If a domain is in /etc/remotedomains it will be removed from /etc/localdomains.
Also, if you have enabled WHM > Tweak Settings > Automatically setup /etc/localdomains, /etc/remotedomains, /etc/secondarymx based on where the mx entry is pointed, then if the configured DNS resolvers are incorrect those files will be updated incorrectly.
To retain control over the files, disable that feature.
- cpanel, exim, local problem, temporary
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