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We critically (re)examine the associated production process of a $J/ψ$ meson plus an open charm hadron at the LHC in the proton-proton ($pp$) and proton-lead ($p{\rm Pb}$) collisions. Such a process is very intriguing in the sense of tailoring to explore the double parton structure of nucleons and to determine the geometry of partons in nuclei. In order to interpret the existing $pp$ data with the LHCb detector at the center-of-mass energy $\sqrt{s}=7$ TeV, we introduce two overlooked mechanisms for the double parton scattering (DPS) and single parton scattering (SPS) processes. Besides the conventional DPS mode, where the two mesons are produced almost independently in the two separate scattering subprocesses, we propose a novel DPS mechanism that the two constituent (heavy) quarks stemming from two hard scatterings can form into a composite particle, like the $J/ψ$ meson, during the hadronization phase. However, it turns out the corresponding contribution is small in $J/ψ+c\bar{c}$ hadroproduction. On the contrary, we point out that the resummation of the initial state logarithms due to gluon splitting into a charm quark pair is crucial to understand the LHCb measurement, which was overlooked in the literature. We perform a proper matching between the perturbative calculations in different initial-quark flavor number schemes, generically referring to the variable flavor number scheme. The new variable flavor number scheme calculation for the process strongly enhance the SPS cross sections, almost closing the discrepancies between theory and experiment. Finally, we present our predictions for the forthcoming LHCb measurement in $p{\rm Pb}$ collisions at $\sqrt{s_{NN}}=8.16$ TeV. Some interesting observables are exploited to set up the control regions of the DPS signal and to probe the impact-parameter dependent parton densities in lead.