Apparently the current behaviour of authconfig is to "take over" the first domain listed in sssd and reconfigure it.
Authconfig shouldn't do that as it will destroy potentially valuable configuration.
Authconfig should always only use "default" as domain name and add it to the list of currently active domains.
This avoid irreparably destroying a currently working configuration if authconfig is misused on a machine that already has working domains configured.
Note: authconfig may decide to rewrite the "domains" option in [sssd] instead of just appending. This will cause the deactivation of other configured domains, but at least it will not destroy their configuration and all a user needs to do is to change back the "domains" option to include the right domains.
Also note: a non working domain does not affect other domains. If a domain fails sssd will go on consulting all the others and will log the issue to the log files.