For U2F there's nothing to be in sync: each key is added individually, and you don't have to add all of them at once. I.e. if you register the key on your keychain at work, you could later add the backup key in your home vault.
For storing TOTP keys on your YubiKeys, those must be the same, so you probably have to add them at the same time, or take a picture of the QR-code before you complete the registration.