In multi-configurational time-dependent Hartree (MCTDH) approaches, different multi-layered wavefunction representations can be used to represent the same physical wavefunction. Transformations between different equivalent representations of a physical wavefunction that alter the tree structure used in the multi-layer MCTDH wavefunction representation interchange the role of single-particle functions (SPFs) and single-hole functions (SHFs) in the MCTDH formalism. While the physical wavefunction is invariant under these transformations, this invariance does not hold for the standard multi-layer MCTDH equations of motion. Introducing transformed SPFs, which obey normalization conditions typically associated with SHFs, revised equations of motion are derived. These equations do not show the singularities resulting from the inverse single-particle density matrix and are invariant under tree transformations. Based on the revised equations of motion, a new integration scheme is introduced. The scheme combines the advantages of the constant mean-field approach of Beck and Meyer [Z. Phys. D 42, 113 (1997)] and the singularity-free integrator suggested by Lubich [Appl. Math. Res. Express 2015, 311]. Numerical calculations studying the spin boson model in high dimensionality confirm the favorable properties of the new integration scheme.