Unless the changes to the roof are significant you should be able to ‘regularise’ the situation, as the planners put it, by submitting an application to approve the new roof details. Talk to a senior planning officer about this immediately. Find out if he or she will accept the revised plans as a minor variation to those permitted, or whether a new application is needed.
Be reassured that although the enforcement officer’s rather alarming analysis is technically correct, the very worst case is that you would have to rebuild the part of the roof you have altered so as to comply with your permission. With that in mind, focus any discussions with planners onto the minor differences between what’s permitted and what has been built and the lack of harm arising from the alterations. A lot is at stake here, and you would be well advised to get help from a planning consultant as soon as possible..

The first question that springs to mind is why does the building not comply with the approved drawings? If your builder has advised you that the changes would be fine, it is their responsibility to sort it out for you. Without knowing how significant the differences are it is not possible to advise you to do anything other than to stop building that part of the project until you have a fairly clear answer from the planners as to what is acceptable. If you want to keep to the changed design, you may need to submit a new planning application, or at least go through the formal process of getting approval for an amendment to the design. By the sound of it your neighbour will be on hand to make sure that the proper procedures are followed.