Magnetic skyrmions are vortex-like topological spin textures often observed to form a triangular-lattice skyrmion crystal in structurally chiral magnets with Dzyaloshinskii-Moriya interaction. Recently $beta$-Mn structure-type Co-Zn-Mn alloys were identified as a new class of chiral magnet to host such skyrmion crystal phases, while $beta$-Mn itself is known as hosting an elemental geometrically frustrated spin liquid. Here we report the intermediate composition system Co$_7$Zn$_7$Mn$_6$ to be a unique host of two disconnected, thermal-equilibrium topological skyrmion phases; one is a conventional skyrmion crystal phase stabilized by thermal fluctuations and restricted to exist just below the magnetic transition temperature $T_mathrm{c}$, and the other is a novel three-dimensionally disordered skyrmion phase that is stable well below $T_mathrm{c}$. The stability of this new disordered skyrmion phase is due to a cooperative interplay between the chiral magnetism with Dzyaloshinskii-Moriya interaction and the frustrated magnetism inherent to $beta$-Mn.