We probe dephasing mechanisms within a quantum network node consisting of a single nitrogen-vacancy center electron spin that is hyperfine coupled to surrounding C13 nuclear-spin quantum memories. Previous studies have analyzed memory dephasing caused by the stochastic electron-spin reset process, which is a component of optical internode entangling protocols. Here, we find, by using dynamical decoupling techniques and exploiting phase matching conditions in the electron-nuclear dynamics, that control infidelities and quasistatic noise are the major contributors to memory dephasing induced by the entangling sequence. These insights enable us to demonstrate a 19-fold improved memory performance which is still not limited by the electron reinitialization process. We further perform pump-probe studies to investigate the spin-flip channels during the optical electron spin reset. We find that spin flips occur via decay from the metastable singlet states with a branching ratio of 8(1):1:1, in contrast with previous work. These results allow us to formulate straightforward improvements to diamond-based quantum networks and similar architectures.