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We study the transition of $ν=1/3$ and $2/5$ fractional quantum Hall states of the honeycomb Hofstadter model as we tune to a two-orbital moiré superlattice Hamiltonian, motivated by the flat bands of twisted bilayer graphene in a perpendicular magnetic field. In doing so, we address the extent to which these states survive in moiré systems and analyze the nature of the transition. Through the use of a Peierls substitution, we determine the Landau-level splitting for the moiré Hamiltonian, and study the structure of the Chern bands for a range of magnetic flux per plaquette. We identify topological flat bands in the spectrum at low energies, with numerically tractable lattice geometries that can support the fractional quantum Hall effect. As we tune the model, we find that the orbital-polarized $ν=1/3$ and $2/5$ states corresponding to the honeycomb Hofstadter model survive up to $\approx 30\%$ of typical moiré superlattice parameters, beyond which they transition into an insulating phase. We present evidence for this through density matrix renormalization group calculations on an infinite cylinder, by verifying the charge pumping, spectral flow, entanglement scaling, and conformal field theory edge counting. We conclude that fractional quantum Hall states from the Hofstadter model can persist up to hopping amplitudes of the same order as those typical for moiré superlattice Hamiltonians, which implies generally that fractional states for moiré superstructures can be discerned simply by analyzing the dominant terms in their effective Hamiltonians.