I've been experimenting with a backup of the portal system and as part of trying to find a different problem by trial and error, I removed nearly all (couple of hundred) modules from the system.

Then I sifted through the bin, the file system and the database and cleared out all the garbage left behind by so many of them.

Then, just out of interest I tried deleting a portal, and now I can delete them without error.

There's a clue in there somewhere but I don't know what it is. Why would clearing out modules all of a sudden allow portals to be deleted again?