In this situation, is the Government still bound by the timeframe dictated in the Prompt Payment provisions (7days to determine whether the invoice is proper, 14 days to make payment) or can a longer review period be justified because of the cost-reimbursable nature of the invoices?
You have listed the clauses well. Make sure they should be prescribed to your contract. That being said, the easy answer would be... the rules governing prompt payments to contractors are pursuant to the Prompt Payments Act and being a statutory requirement they are to be followed regardless of the difficulty of reviewing the documentation supplied by the contractor.
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The documentation is a point where your agency may be able to negotiate a more concise series of supporting documentation from the contractor. Based on the information you have provided on your contract it seems like your agency may have made their bed by not understanding the massive report requirements. This isn't the fault of the contractor. They may be relieved if your agency does not require an unreasonable level of detail moving forward. It is probably a large effort on their part, as it is on your part.
Please use caution when limiting detail in supporting documentation that may be necessary to make a correct decision when approving invoices. Make sure that you discuss this with the contract's Program Manager and COR, as well as, your Contracting Officer as they may require a certain level of detailed reports even if they are burdeonsome. Obviously, it is not in your best interest to make a unilateral decision that will negatively affect the mission of the program office in line with their contract.