Upon receipt of a stop work order you have no guarantee of payment for any transaction date-stamped in your accounting system after the date of the stop work order (or the commencement date of a stop work order specified in a Contracting Officer's Letter).
I suggest clients receiving these orders close the charge numbers applicable until the stop work order is lifted with an order to resume effort and immediately notify any effected suppliers and subcontractors to do the same.
To the degree the government has not paid anything on the contract or delivery order they have no ownership rights to the product and you are free to complete it and sell it to another customer (commercial or government) that has not stopped work. If the government recommences the order, quote a new price and delivery from ground zero.
At the bottom line a stop work is blunt and to the point. Treat it as if you will never hear from this customer again to manage the risk.
To the degree you do hear from the CO again and he or she has the funding to recommence work, be prepared to submit a proposal for what it will take to start the effort and a realistic delivery schedule to complete the it, but do not build any retroactive costs incurred during the stop work period into your logic and expect to bill them; they may not come to payment fruition.
Hypothetically at some future date the government could terminate the contract without taking delivery and the contractor will then submit a termination proposal for recovery of costs and disruption.
At that time, you should inform the government that you are pleased to resume work, but under revised price and delivery conditions as specified in a proposal for equitable adjustment
You should not resume work until a contract or work order amendment is received granting the price and delivery relief to contract requirements commensurate with negotiation results under your proposal for equitable adjustment.