The problem bugged me and I kept investigating. To debug, I enabled the DNS-zone and actually transferred it with AXFR to an external server. There I realized, that the SOA-record was bit strange. Further trials reveald that in the NS-records, there was always an extra one. With that in mind, I went directly to the database to see what I had stored there for the zone.
And what do you know! There were two IDs for the given name. That is a big no-no. It's like you having two heads. A freak of nature. It cannot happen. It is so illegal, that there aren't even laws about it. To fix that I did rename the one with a smaller ID:
UPDATE dns_zone SET name = '-the-zone-_obsoleted', displayName = '-the-zone-_obsoleted' WHERE id = -the-smaller-ID-;
After that a manual refresh of the BIND records from the DB: