Whilst your intent is honourable, the Local Authority does not always see it your way.
If they have stipulated these requirements, whether previously agreed otherwise this there is little that you can do. We have tried to negotiate on behalf of clients, but they have been served with notices to remove all of the works and put it back to its original state.
The best way is to comply with their request.
We can provide you with a service, to provide retrospective planning and Building Regulation consent. We are here to help in this situation and take up your case on your behalf. You can use a local architect, but please check out our services as well.