passwd changes the password of the key that was used to access the repository. If each key has a unique password, then the correct key is already selected for the password change. If you have multiple keys with the same password, then you probably want to use --key-hint key with the id of the key to change. Or just remove one of the duplicate keys and add a new one.
Edit:
All keys are wrappers for the actual master key. As there is only a single master key for each repository, all keys are interchangeable.