Is there a FAR or DoD regulation that prohibits the split procurment of initial spares?
There are no known DOD Financial Management Regulation 7000-14.R prohibitions to procuring initial spares in split purchases. The Fiscal Year requirement for initial spares is identified annually in the P-40 Budget Item Justification Sheet as a part of the President's Budget Submission to Congress. The initial spares value is directly associated with the procurement quantity and dollar value approved by Congress each FY. It is then incumbent upon the procuring activity to efficiently contract for the end items and initial spares as approved.
Although it may be inefficient and not in the best interest of the government to procure the total fiscal year spares with two procurement actions, there is nothing to preclude the action. The second purchase of initial spares in the FY must also be made with the approved Procurement funds. Purchases of replacement spares are typically funded with the Operations and Maintenance appropriation. Guidance for funding initial spares may be found in the FMR in Vol 2A, Cha 1 and Vol 2B Cha 4. http://comptroller.defense.gov/fmr/current/02a/02a_01.pdf
You are encouraged to discuss this action with the cognizant procuring activity, Contracting Officer and Comptroller.