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"Service Temporarily Unavailable
The server is temporarily unable to service your request due to maintenance downtime or capacity problems. Please try again later."
I get this message on mail.mynewdomain.com/webmail and mail.mynewdomain.com/sac, but not on mail.mynewdomain.com/Scalix/rw (which works fine).

What I did was change the hostname using the description in the Scalix Administration Guide: http://www.scalix.com/documents/Scalix_ ... 11.0.2.pdf
which is different (as I found out later) from the description here: http://www.scalix.com/wiki/index.php?ti ... ChangeFQDN

Instead of trying to find the needle in the haystack (a small typo somewhere?) I am now ready to completely uninstall Scalix; then reinstall it using the right hostname and /etc/hosts content.

There is information here on uninstalling Scalix and automatically importing old data: viewtopic.php?p=36506
But I would prefer to export all mailboxes and users; remove Scalix including all data; then do a clean install and import mailboxes and users.

Any suggestions on what would be the best/easiest/most logical way of doing this?

The problem there is that tomcat is probably not running, or running with incorrect settings. A look through /etc/opt/scalix-tomcat and /var/opt/scalix/??/tomcat will probably pinpoint the issue.

If you want to go the uninstall/reinstall route, uninstall everything except for the Scalix Server, check that /etc/opt/scalix and /etc/opt/scalix-tomcat is deleted, as well as everything in /var/opt/scalix/?? EXCEPT for /var/opt/scalix/??/s, then re-install the components.

Alternatively you can use the installer to reconfigure all the components.

I backed up everything; used the mbox backup script from the wiki; then used the installer to uninstall 11.0.2.
After that I installed 11.0.4 using the installer. It did not work "Server not running" when accessing mydomain.com/webmail. omrc helped; apparently even after the reboot the server did not start up. I haven re-rebooted yet to see why the server did not come online after the boot.
Anyway, we are emailing again.
Thanks for your comments.