Hi,
There is an script located at '/usr/share/zentyal/smart-admin-report' that checks the status of a Zentyal, that script contains a function called 'dc_check' that do several checks in the Domain Controller module, perhaps you should run the script in both Zentyal and check the results.
Also, there is a command 'samba-tool showrepl' that you should run in both servers in order to check the replication status.
Finally, did you analyze the log files in both servers? Perhaps, the replication has some kind of issue.
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