Due to the problem of consistency between the matrices in Equation 6 arising from a) enforcing reversibility and b) data splitting for cross-validation, we recommend that VAMP2(k) scores, either cross-validated or bootstrapped, should not used for reversible and stationary MSMs. Instead, we recommend bootstrapping the sum of the squared eigenvalues (VAMP2 eq (k)) directly from the reversible transition matrix. This has the same theoretical properties of the VAMP2(k) score (i.e., represents captured kinetic variance, and link to variational theorem) while not a) wasting data due to data splitting and b) perfect correlation with the implied timescales.