I didn't really find much in the DB to delete, so I decided to delete the first entry that I was still able to delete in ISPConfig, and the second one (same co-domain in another web) disappeared with it.
Then I received lots of errors. I emptied the recycle bin, logged out and in again. Now I was able to add the co-domain to the right web, and it seems to be working.
Very strange...
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