If you use File>Sync>with External Folder, internal changes to the software require that you create a new external folder to sync with in Scrivener 3.
The developer recommends that you take the following steps.
1. Sync the project one last time in Scrivener 1 to ensure it’s fully up to date.
2. Delete the external folder you were syncing with.
3. Open the project in Scrivener 3, which will upgrade it to the new project format.
4. Create a new external folder and sync to it.