Noise can have severe impacts on particle beams in high-energy synchrotrons. In particular, it has recently been discovered that noise combined with wakefields can cause a diffusion that leads to a loss of Landau damping after a latency. Such instabilities have been observed in the Large Hadron Collider. This paper, therefore, studies the beam response to noise in the presence of wakefields, within the framework of the Vlasov equation. First, a wakefield beam eigenmode transfer function (MTF) is derived, quantifying the amplitude of a wakefield eigenmode when excited by noise. Then, the MTFs of all the wakefield eigenmodes are combined to derive the beam transfer function (BTF) including the impact of wakefields. It is found to agree excellently with multi-particle tracking simulations. Finally, the MTFs are also used to derive the single-particle diffusion driven by the wakefield eigenmodes. This new Vlasov-based theory for the diffusion driven by noise-excited wakefields is found to be superior to an existing theory by comparing to multi-particle tracking simulations. Through sophisticated simulations that self-consistently model the evolution of the distribution and the stability diagram, the diffusion is found to lead to a loss of Landau damping after a latency. The most important technique to extend the latency and thereby mitigate these instabilities is to operate the synchrotron with a stability margin in detuning strength relative to the amount of detuning required to barely stabilize the beam with its initial distribution.