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It is still hard to understand why a system needs to adapt to such a wide range of battery packs, and why a single battery pack must be used for all of the power requirements. Without a detailed specification of all parameters, we are just playing a shoot-in-the-dark game, and being fed pieces of the puzzle. If this is classified, this is not the place to leak bits and pieces of possibly sensitive information. If not, I would be interested in seeing the full specifications for at least this portion of the design.
I am guessing that there may several sizes of drones with different battery packs, and maybe one or more packs of various sizes for each, based on mission requirements. Also, I am guessing that the battery pack(s) are used to drive one or more electric motors for propulsion, and also for communications, video devices, GPS, guidance control, environmental sensors, data collection equipment, etc. All of these probably have different power and voltage requirements, and would have different priorities of reliability and running time. I think it would be foolish to rely on a single battery pack with such a wide range of voltages for all functions.
The electronics should be easily standardized to use 12 VDC, and it would be prudent to have two such packs with a system to provide a backup in case of failure. The propulsion power should be a separate pack, and I would suggest having one for emergency use, and then one or more main packs which may be sized or connected in parallel as required for the mission.
Of course, all of this assumes that you have control of the entire project. Most likely, if you are working as part of a DOD team, the overall specifications were determined long ago and set in concrete by clueless politicians and bureaucrats, and now you must make your design work within possibly unreasonable constraints.
You may deposit my $10,000 consulting fee for your defense project in my PayPal account :)
Paul E. Schoen