NEC ECC: Liability for an uncorrected Defect

I understand the principle behind clause 45 and that the PM "assesses" the cost of correcting a Defect but if the Employer decides to have a third party correct the Defect does this mean that the Contractor will no longer be accountable for that element of the work should a latent defect/issues appear at a later stage?

Obviously, the Contractor's argument will be should a latent defect/issue appear it is not his responsibility or fault and any issue is down to the work carried out by the third party.