I've cracked it. I'm not sure if there are any bugs involved, or if I just don't really understand the auth system, but
First, when you sign in to either the UI or the shell, it seems to revoke your (root?) key for the other one. Logging out and back in to the other will refresh your view there.
Second, this revocation is only for the applicable domain/region group you signed into. In the case of the UI this is all of them, while in the case of the shell, this is always 'Classic' (I tried fauna cloud-login --domain db.us.fauna.com
but doesn't seem to work - ~/.fauna-shell
still shows domain=db.fauna.com
and the key is valid for Classic). This means you are still logged into the dashboard, but all of the 'Classic' databases disappear from view.
Third, while in the state mentioned above, you are able to create a new database in the US or EU region group, but not Classic (attempting will result in this error). You then remain logged into the shell with the Classic databases listed, and logged into the UI but having your Classic access revoked.
You're now seeing what I saw -
fauna list-databases
shows all databases in the Classic region group, while the dashboard UI shows all databases NOT in the Classic region group.
Logging out and back into the site will result in all databases being shown. Logging back into the shell will only ever show the Classic region group databases.
** Edit ** Attempting to login to a region group:
bash-3.2$ fauna version
fauna-shell/0.12.4 darwin-x64 node-v16.1.0
bash-3.2$ fauna cloud-login --domain=db.us.fauna.com
For email login, ...<truncated>
Email or secret key: <email>
Password: ***************
The 'cloud' endpoint already exists. Overwrite? [y/n]: y
bash-3.2$ fauna list-databases --domain=db.us.fauna.com
› Error: Could not Connect to https://db.us.fauna.com Unauthorized Secret
bash-3.2$ fauna list-databases
listing databases
tsukiyomi