I realize there will still be a conference to resolve differences. But, assuming the SAC-D position sticks, can we buy missiles with the funds that were reinstated or not?
If the SAC-D position sticks and it is the final outcome in the conference committee, then you may be held to the reduced quantity. The HASC/SASC are the authorizers so they approve quantities, personnel levels, and approve programs. They also recommend funding. It is the appropriators who provide the funding levels and hence, budget authority. If the authorizers approve the higher quantities and the appropriators approve the higher funding, then you should be OK.
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However, if there is a disconnect between the authorizers and appropriators OR the final appropriation bill has the disconnect you have outlined above (enough money but not approval for the quantity), then it is common practice for the legislative liaison and OSD Comptroller to request clarification so that we implement according to Congressional intent. In all likelihood, the disconnect will be resolved at conference, but if not, it could take some time to resolve by querying Congress. Recommend your office initiate discussions with your PEM and OSD POC to see what their intentions would be to follow up if the disconnect remains. This is one of those questions where there isn't a clear cut answer.