ABSTRACT We present a new suite of cosmological zoom-in hydrodynamical ($\approx 20\, \mathrm{pc}$ spatial resolution) simulations of Milky-Way mass galaxies to study how a varying mass ratio for a Gaia-Sausage-Enceladus (GSE) progenitor impacts the z = 0 chemodynamics of halo stars. Using the genetic modification approach, we create five cosmological histories for a Milky-Way-mass dark matter halo ($M_{200}\approx 10^{12} \, \mbox{M}_\mathrm{\odot }$), incrementally increasing the stellar mass ratio of a z ≈ 2 merger from 1:25 to 1:2, while fixing the galaxy’s final dynamical, stellar mass, and large-scale environment. We find markedly different morphologies at z = 0 following this change in early history, with a growing merger resulting in increasingly compact and bulge-dominated galaxies. Despite this structural diversity, all galaxies show a radially biased population of inner halo stars like the Milky-Way’s GSE which, surprisingly, has a similar magnitude, age, $\rm Fe/H$, and $\rm \alpha /Fe$ distribution whether the z ≈ 2 merger is more minor or major. This arises because a smaller ex-situ population at z ≈ 2 is compensated by a larger population formed in an earlier merger-driven starburst whose contribution to the GES can grow dynamically over time, and with both populations strongly overlapping in the $\rm Fe/H-\rm \alpha /Fe$ plane. Our study demonstrates that multiple high-redshift histories can lead to similar z = 0 chemodynamical features in the halo, highlighting the need for additional constraints to distinguish them, and the importance of considering the full spectrum of progenitors when interpreting z = 0 data to reconstruct our Galaxy’s past.