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NASA’s Lunar Flashlight (LF) and Near-Earth Asteroid (NEA) Scout CubeSat missions are planned to launch in 2022. Lunar Flashlight is a low-cost secondary payload concept that will map the lunar South Pole for volatiles and demonstrate several technological firsts, including the first planetary CubeSat mission to use green propulsion, and the first mission to use lasers to look for water ice. NEA Scout is a low-cost concept that will map an asteroid and demonstrate several technological firsts, including being the first CubeSat to reach an asteroid. Flight software for both CubeSat missions is based on the open-source F Prime Flight Software Product Line developed by JPL. F Prime utilizes a reusable component-based architecture with typed ports that can be interconnected to form a topology. Also, F Prime includes a set of auto-coding tools used to generate components and topologies that can be deployed for various mission specific applications. Both CubeSats share a common set of avionics for command and data handling (C&DH), telecom and power. This commonality in hardware is translated to a shared deployment in software enabling concurrent flight software development for both CubeSats. The modularity and reusability in F Prime enable such concurrent flight software development for different applications given a common set of avionics. In particular, F Prime has been used successfully to develop a common software deployment for the Sphinx C&DH platform used on both CubeSats. The common F Prime deployment for Sphinx has also been made open source to provide a starting point for any future F Prime software deployments utilizing the Sphinx platform. This paper provides a comparison between the Lunar Flashlight and NEA Scout Flight Software deployments highlighting the use of a common shared set of F Prime components developed for the Sphinx platform along with general lessons learned for CubeSat flight software development with the F Prime Framework.