This response is based on the information provided.  We suggest you discuss with your contracting and finance team, program manager and/or legal department as appropriate.

If the funds are still properly obligated on the contract, the funds can be paid out even though they are expired for new obligations.  If the services performed are related to the contract and being executed within the scope and period of performance of the contract then, again, the contractor can be paid with those funds.  We believe you are referring to specific task direction given by the Navy after funds ae obligated.  Again, if the specific task is within the original scope and period of performance, the funds are valid for payment.

We are unclear as to what you mean when referring to " command is issuing funding documents this way".  Once obligated to the contract, there should be no other internal (off contract) manipulation of funds.  Funds sent from an organization to the NWCF would maintain the Appropriation's characteristics, i.e. O&M period for new obligations is 1 year, RDT&E period for new obligations is 2 years, etc.   Once an Appropriation enters into an Expired period no new obligations may be created, only payment of invoices and obligation adjustments are permissible.