Validity of a NEC3 PMI

Would a Project Managers instruction that also indicated it was a compensation event validly reverse a main clause in the NEC Contract? Should it not have been a variation to the contract explicity agreed between the parties, or is the ‘die cast’?

The PM can only instruct a change to the works information, not contract clauses.
As you suggest, amending the contract clauses can only be done by agreement of the contractor and client, the PM administers the contract as agreed.