Assuming that the 10 weeks is added to the 80 weeks to give a total duration of 90 weeks, then the payment assessment procedure would value the work based on the definition of Price for Work Done to Date, which is either the completed BoQ quantity or a proportion of a lump sum item.
You could pay against the 10 weeks for the Site Manager and Engineer if it relates to a period of delay at that point in time, but that would have the effect of pushing back the rest of the 80 weeks by 10 weeks. You wouldn't pay both at the same time.
It sounds like the Subcontractor is 'either trying it on' or they have potential cash-flow issues.