UPDATE: Well, once you restore the old Aperture library, iTunes sees it and allows you to sync the iPhone to it.
When you migrate your existing Aperture library to the new Photos app, it does away with all the Aperture Projects. So, all my old organization was gone.
Luckily, there's a way to recover the old Aperture library. In ~/Pictures, all the migration did was to rename the "Aperture Library.aplibrary" file to "Aperture Library.migratedaplibrary". Just Get Info on the file, and modify the extension. Open Aperture, and see all your old stuff return.
I have not figured out how to get the iPhone to revert to syncing with the Aperture library rather than the Photos library. 😡