Recently, it has been suggested that the dearth of small halos around the Milky Way arises because of a modification of the primordial power spectrum of fluctuations from inflation. Such modifications would be expected to alter the formation of structure from bottom-up to top-down on scales near where the short-scale power has been suppressed. Using cosmological simulations, we study the effects of such a modification of the initial power spectrum. While the halo multiplicity function depends primarily on the linear-theory power spectrum, most other probes of power are more sensitive to the nonlinear power spectrum. Collapse of large-scale structures as they go nonlinear regenerates a "tail" in the power spectrum, masking small-scale modifications to the primordial power spectrum except at very high z. Even the small-scale (k > 2 h Mpc(-1)) clustering of the Ly alpha forest is affected by this process, so that cold dark matter (CDM) models with sufficient power suppression to reduce the number of 10(10) M. halos by a factor of similar to 5 give similar Ly alpha forest power spectrum results. We conclude that other observations that depend more directly on the number density of collapsed objects, such as the number of damped Ly alpha systems or the redshift of reionization, may provide the most sensitive tests of these models.