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Is there a way I can simply re-associate the mail server with the main server in the setup?
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No.
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What would happen if I uninstall ISPConfig from the mail server and then reinstalled? Would I have to recreate the email domains and mailboxes through the ISPConfig administration panel on the main server or would the data in the database get mirror onto the server once reinstalled?
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You would have to delete all meail domains and accounts first and then recreate them on the new server. So thats not a real option.
You might want to consider to contact our ispconfig support instead as such a problem can always be fixed without a reinstall.
http://support.projektfarm.com