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Nanoelectronic quantum dot devices exploiting the charge-Kondo paradigm have been established as versatile and accurate analog quantum simulators of fundamental quantum impurity models. In particular, hybrid metal-semiconductor dots connected to two metallic leads realize the two-channel Kondo (2CK) model, in which Kondo screening of the dot charge pseudospin is frustrated. Here, we consider theoretically a two-channel charge-Kondo device made instead from graphene components, realizing a pseudogapped version of the 2CK model. We solve the model using Wilson's Numerical Renormalization Group method, and uncover a rich phase diagram as a function of dot-lead coupling strength, channel asymmetry, and potential scattering. The complex physics of this system is explored through its thermodynamic properties, scattering T-matrix, and experimentally measurable conductance. We find that the strong coupling pseudogap Kondo phase persists in the channel-asymmetric two-channel context, while in the channel-symmetric case frustration results in a novel quantum phase transition. Remarkably, despite the vanishing density of states in the graphene leads at low energies, we find a finite linear conductance at zero temperature at the frustrated critical point, which is of non-Fermi liquid type. Our results suggest that the graphene charge-Kondo platform offers a unique possibility to access multichannel pseudogap Kondo physics.