The problem seems to be solved. The superuser belonged to the publisher group which has read only access to the website. When I removed the superuser from that group it seemed not to have immediate influence on the export behaviour although the permission list was correct. So when the export suddenly worked I didn't linked it to the group change. But later on I remembered that group change and tried to export the superuser and add him to bootstrap. After restarting magnolia the export of the website was immediately available for the superuser.
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