This response is based on the information provided. We suggest you discuss with your contracting team, program manager and/or legal department as appropriate.
If the contract or specific CLINs on the contract expire you would need to create new CLINs assuming the contract itself had not expired. What you can do is extend the period of performance of the CLINs in question based on the when you expect to get the funding. Once you get the funding you will need to again modify the contract and extend the period of performance.
If the CLINs are FFP you have less risk as the contractor is not likely to spend its money. If the CLINs are some manner of cost reimbursement, you must be explicit in telling your contractor not to perform until funding is added. If the contractor performs at risk it has a supportable argument for a claim if the government is aware and does not direct the contractor to stop. Telling the contractor, "You perform at your own risk until funds are added to the contract" and then ignoring the contractor performing exposes the government to liability.
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