Jail upgrade from 11.2-RELEASE-p15 to 11.3-release fails

I updated my FreeNAS installation from 11.2-U7 to 11.3-RC1. This did work fine.

Then I tried to upgrade a jail from 11.2-RELEASE-p15 to U11.3-RELEASE. I got messages like

The following file could not be merged automatically: /etc/freebsd-update.conf
Press Enter to edit this file in /usr/bin/vi and resolve the conflicts
manually...

and when continuing I was not able to login. See also 

https://www.ixsystems.com/community/threads/freenas-11-3-beta-1-how-to-update-jails-from-11-2-to-11-3-release.80147/ 

which describes the same issue as I experienced.