We present a robust protocol to reshape interactions in a spin ensemble based on global control pulse sequences applied to multiple subensembles in parallel. This setting arises naturally from ensembles of solid-state defects or multi-species atomic a
We present a robust protocol to reshape interactions in a spin ensemble based on global control pulse sequences applied to multiple subensembles in parallel. This setting arises naturally from ensembles of solid-state defects or multi-species atomic arrays. We show that it is provably computationally hard to find pulse sequences that simultaneously engineer interactions both within and between subensembles. Despite its formal hardness, we identify a set of necessary or sufficient conditions under which one can synthesize a target Hamiltonian from the native one. Moreover, we introduce efficient numerical strategies for designing pulse sequences that engineer target Hamiltonians robust against common control imperfections. As a specific application, we discuss the robust generation of two-mode spin squeezing in dual-species atomic ensembles, which is a challenging task without subensemble control. Our results provide a practical toolbox to design novel quantum simulation and sensing experiments with minimal control overhead.