Yubikey recommends "having a backup device and registering both with your accounts". I vaguely remember some people saying that they have a backup Yubikey that they keep in their safe deposit box, so that it's as safe as possible.
I could see this working for a few very secure logins, but if the idea is to two factor everything it doesn't seem tenable.
you add your main device and your backup device.
than you store the backyup device, after having it configured on your accounts, in the safe and use the main device to authenticate on a daily basis.
when you create a new account you add your main device and than when possible retrieve the backup device from storage and add the new account to it and store it back again.
on the event of you loosing your main device you retrieve the backup device from storage, use it to authenticate and remove your lost device from your accounts.
You can then acquire a new one key, add to all your accounts and store the backup in a safe again until needed.