A recent paper in this journal described the identification and integration of sources of risk in a systems engineering process model [Lambert, Jennings, and Joshi, Syst Eng 9(3) (2006), 187–198]. The earlier effort falls short in addressing sources of deep, nonprobabilistic uncertainty that should enter to strategic systems design and reengineering. Our new paper incorporates the earlier effort to a framework for evaluating which are the deep uncertainties that most influence a priority‐setting among investments in large‐scale systems with multiple stakeholders, and therefore warrant more investigation. The framework addresses that deep uncertainties are continuously discovered and reflective of diverse and unique stakeholder experiences, knowledge bases, and advocacy positions. Deep uncertainties are epistemic viewpoints across which the strategic priorities for investments will differ. The framework modifies existing tools of scenario analysis and multicriteria analysis to process and filter the deep uncertainties. The framework is demonstrated in an application to reengineering of an energy system for a defense installation where frequent outages are disruptive to scientific and other missions. The sources of deep uncertainty in the demonstration include regulatory, economic, environment, cyber‐threat, and others. The investments include innovative microturbine and microgrid technologies. An example of a result is that international economic disruption is relatively more influential than cyber‐threats to strategic priority‐setting for investing in a microgrid at the particular installation. ©2012 Wiley Periodicals, Inc. Syst Eng 15