Okay, repair followed by a verify (both of which detected errors) fixed it.
The good news is that Duplicati has robust error handling and can recover. In my experience it also detects issues so even if it can’t fix them automatically it does let you know.
The bad news is that I had to do a full verify to fix, which meant downloading everything. This was a small set so no problem but for large ones… Well my advice would be to break your sets up into smaller ones.