If there has been an excess, is the Project Manager’s assessment of the Contractor’s share deducted from the amount due on termination?

If there has been an excess, is the Project Manager’s assessment of the Contractor’s share deducted from the amount due on termination?

Yes. The Project Manager’s assessment of the Contractor’s share is deducted from the amount due to the Contractor on termination if there has been an excess (see Clause 93.6).