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Resolved
Cpanel Support found the problem with our case for all interested:
For some reason these domains are in the /etc/remotedomains file
which causes them to not be added back to /etc/localdomains when mailperm is run. If the mx servers for those domains are indeed supposed to be the server itself the delete those domains from there and add to /etc/localdomains, they should not be deleted on subsequent mailperm runs.
cPanel.net Support Ticket Number:
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