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We report a method of engineering a reversible change in interlayer bonding between layers of exfoliated thin films of MoS2 by means of hydrogen intercalation through forming gas annealing. Interlayer bonding strength is probed through the behavior of MoS2 under process-induced strain engineering, where two-dimensional (2D) flakes are encapsulated with a deposited stressed thin film layer to transfer strain into the underlying 2D materials. It is shown that after forming gas annealing, the depth of the strain transferred into multilayer MoS2 is enhanced as determined through layer-thickness-dependent Raman spectroscopic mapping. This change represents a transition from a 2D van der Waals-bonded material in the as-exfoliated samples to a more three-dimensional (3D)-bonded system in the annealed samples. We demonstrate the reversibility of this effect by means of vacuum annealing of previously forming gas annealed samples. The process of forming gas annealing itself also imparts strain into MoS2 due to a combination of 2D-to-3D bonding transition with differential thermal mismatch between the MoS2 and the substrate. These strains are shown to be retained after the vacuum annealing process, despite the transition back to 2D bonding. Since forming gas annealing is a common technical process in engineering 2D electronic devices, these results represent an important consideration in understanding non-intentionally applied strains due to changes in the mechanical properties of 2D materials.