NEC ECC: Termination & Pain Gain calculation

Under an NEC3 ECS Main Option C, If the works were terminated by the Contractor or Subcontractor, will the pain gain mechanism still apply to the final amount due?

Yes. Main Option C adds clauses 93.4 and 93.6 which detail how the share amount is assessed, which is then added (or deducted as the case may be) to the calculated total.