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What does the builder say about this?What does the lawyer and bank say?Do you want to get out because there are problems with the house?
So from what you are saying the builder failed to provide you what you were paying for and as such you have a strong case against the builder if you were to sue. That means the builder will likely be found liable.
But if you have not suffered damages then the builder will not be ordered to pay any.
Your next step should be to either demand that the builder do what is necessary to acquire the permit or else have your lawyer make the demand.
Does that answer your question?