Is this an ADA violation? Does this constitute a need for a stop work?
The "Bottom Line Up Front" (BLUF) is that the problem you are facing is not an Anti-Deficiency Act (ADA) violation since it does not involve the use of U.S. Government DoD funds authorized and appropriated by Congress. The question background makes it reasonably clear that only Foreign Military Sales (FMS) case funding is involved, and FMS case funding is not authorized or appropriated by Congress so ADA compliance is not an issue.
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The more fundamental problem described involves how to resolve overspending on one FMS LOA line (Ground Station) and a significant administrative delay in moving funding from another FMS LOA line (Air Vehicle) to provide sufficient funding to pay the contractor for work performed under the UCA contract.
Per the SAMM and FMS LOA implementation practice, the only practical solution is to amend the FMS LOA to 'move money' from the Air Vehicle FMS LOA line to the Ground Station FMS LOA line to provide the funding necessary to pay the contractor the entire $11M invoiced and owed for the Ground Station work performed. (The only other viable option would be to amend the FMS LOA to increase total funds by adding additional foreign customer funds to the Ground Station FMS LOA line, which would be sub-optimal since it's easier to 'move' money from another FMS LOA line in the case to cover the shortfall, which is the course of action you are pursuing.) Until this is FMS LOA modification is completed, the contractor will have to wait for payment (which could, of course, cause other contractual problems).
Accordingly, DAU recommends you contact your Air Force Security Assistance Implementing Agency -- SecAF/International Affairs -- through the AF Security Assistance 'chain of command' to accelerate what should be an relatively simple FMS LOA modification to administratively transfer FMS case funds from the Air Vehicle FMS LOA line to the Ground Station LOA line to provide the necessary funding to pay the contractor invoice for Ground Station work performed. Working aggressively within the AF Security Assistance 'chain of command' to reduce the current 8 month LOA modification timeline to something more reasonable (e.g., 1-2 months) would be the best course of action.