In reading FAR, Part 31 it appears the contractor is not able to claim the items in the scenario as they appear to fall under "Common Items" as they could reasonably be reused on other work.
Question #1 - Does FAR Part 31 take precedent for contract services deemed commercial IAW FAR Part 12 or does another FAR reference control such as Part 12, 49 or 52? FAR part 49 states it can be used as a guide for commercial items.
Question #2 - There appears to be plenty of case laws that would imply that common items are subject to reimbursement under T4C actions where the contractor can argue the costs as reasonable and incurred before termination where the costs cannot be amortized of the life of a contract. Is there something within the T4C clauses that disputes this?
1) FAR 12.102(c) gives FAR Part 12 precedence over other FAR parts when there may be an inconsistency between the parts. Paragraph l (Termination for the Government’s convenience) of the clause at FAR 52.212-4 states "...the Contractor shall be paid...reasonable charges the Contractor can demonstrate to the satisfaction of the Government...have resulted from the termination." That is the guiding principle for your situation.
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2) See the response for #1.