The “disappearing polymorph” phenomenon is well established in organic solids, and has had a profound effect in pharmaceutical materials science. The first example of this effect in metal‐containing systems in general, and in coordination‐network solids in particular, is here reported. Specifically, attempts to mechanochemically synthesize a known interpenetrated diamondoid (dia) mercury(II) imidazolate metal–organic framework (MOF) yielded a novel, more stable polymorph based on square‐grid (sql) layers. Simultaneously, the dia‐form was found to be highly elusive, observed only as a short‐lived intermediate in monitoring solvent‐free synthesis and not at all from solution. The destabilization of a dense dia‐framework relative to a lower dimensionality one is in contrast to the behavior of other imidazolate MOFs, with periodic density functional theory (DFT) calculations showing that it arises from weak interactions, including structure‐stabilizing agostic C−H⋅⋅⋅Hg contacts. While providing a new link between MOFs and crystal engineering of organic solids, these findings highlight a possible role for agostic interactions in directing topology and stability of MOF polymorphs.