Let M 1 and M 2 be compact, orientable 3-manifolds with incompressible boundary, and M the manifold obtained by gluing with a homeomorphism φ : ∂M 1 → ∂M 2 . We analyze the relationship between the sets of low genus Heegaard splittings of M 1 , M 2 , and M , assuming the map φ is "sufficiently complicated." This analysis yields counter-examples to the Stabilization Conjecture, a resolution of the higher genus analogue of a conjecture of Gordon, and a result about the uniqueness of expressions of Heegaard splittings as amalgamations.