Where the town and units assigned to that SHQ?
That also is important. And not all of that happens automatically.

that too, yes.

I tried opening the save file and hitting next turn, and the issue is now resolved. I sent an email for completeness, but it is no longer an active bug! I last ...

This is late feedback, but the new rivers and lakes algorithmic generation is great. The rivers 'make sense' in a way that they didn't before, and create more opportunities for interesting tactical positions.
I had an SHQ bug (?) in my last campaign. After absorbing a non-adjacent city state invaded ...