A: The 2004 Premises Costs Directions do allow this extra reimbursement under paragraphs 46 (payment in respect of running costs) or 47 (financial assistance towards service charges).
However, these elements need to be agreed as part of the overall initial scheme. Having considered an application to include them and taking its budgetry targets into account, the PCT may grant such an application.
LIFT projects do historically have high service charge costs because they include additional facility management elements (such as areas shared by tenants). So it is not unusual for a PCT to agree, as part of a LIFT project, to reimburse all or part of a practice's service charge.
I think the problem that you have is that, because you did not initially apply for service charge reimbursement, it is now not in PCT's budget and thus is not a sum it can afford to pay.