There will be options in the desktop wallet apps to only change certain public keys, so that an account is not tied completely to the hardware wallet.
For example a curation bot may need to store plain text private posting key on a server. They have the option to only change their active and owner public keys, so that funds may only be accessed through the hardware wallet, but able to comment/vote with the posting key like how we're doing it now.
An account may also have more than one public key associated with a particular authority. For example there may be 2 public keys that is associated with posting authority, in which transactions that only require posting authority can be signed with the hardware wallet or another private key.