Is there any update to the answer?
The answer is most likely, no. I assume that your MS B decision was delayed and this is why you are in this situation. I'm not sure whether the risk reduction efforts you mention are actually efforts you would have completed after MS B or they are unfinished business from the pre-MS B activities. Either way, it appears that you have a problem.
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If it is unfinished business then it should be funded with whatever source of funding you used for your pre-MS B activities, including in-house costs. If it is really post MS B effort then you should not be conducting it until you have a decision. I would guess that the description/narrative in the R-2 (and other supporting budget exhibits) that went forward justifying your request for the 6.5 funding clearly stated that the funds would be used for SD&D (post MS B effort). If that is the case I find it hard to think of good justification for using these funds prior to a successful MS B decision. That is, unless there were specific words in your R-2 that described your risk reduction effort and that it may be conducted BEFORE MS B. If these words were included and Congress subsequently appropriated the dollars without taking issue with those words, then you could make a good case for using the funds now. However, I suspect that such words were not in your R-2 and therefore I believe you cannot, in good faith, use the funds until you've
successfully passed MS B. One could even make a case that it would be a Misappropriation Act violation.
The only addition to this answer is since each service has more specific guidance, you need to contact the Comptroller for your organization to ensure you follow the agency specific guidance.