When the PCO issued the definitizing contract, they did not include all sections of the contract. When asked about it, they stated there were no changes to those parts so they were not included in the definitization modification, but are still valid. I thought all parts of the contract needed to be definitized, not just sections that were changed.
Letter contracts are discussed in FAR 16.603. A letter contract is normally issued due to urgency, where there is insufficient time for a Contractor to prepare a proposal and for the Government to evaluate the proposal and negotiate a contract price. FAR 16.603-2(a)(2) requires that a "letter contract should be as complete and definite as feasible under the circumstances."
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In the situation described, the PCO issued a letter contract that included all contract sections A-J. When the letter contract was definitized, the PCO definitized the price (Sections A and B) and made changes to other contract Sections. Although changes were not made to Sections D, E, F, H, and I, these Sections are still valid under the contract as they were included in the original letter contract. There is no requirement for the PCO to revisit Sections that are not changed by the definitization.