If the alternative design was accepted at tender stage, the parties should have removed the redundant requirements from the employer’s works information before the contract was entered into. As that did not happen this is not an ambiguity, but it is an inconsistency in that one part of the works information is not consistent with another part. In that case you as project manager are required to give an instruction to change the works information to resolve the inconsistency.
Given that both parties are agreed that the contractor’s works information is accepted, you should issue an instruction removing the inconsistent requirements from the employer’s works information. Again, given that both parties agree that the contract is in error, this will be treated as being a compensation event which does not change the prices, the completion date, or any key dates.