I only have the tiniest knowledge of the literature on this, but I've taken part in several EEG experiments that tested auditory entrainment, so maybe I can contribute something. Ready your pinch of salt. I reckon that if the change is gradual/slow enough, your neural entrainment should keep pace with the auditory stimulus. However if there's a relatively large, instant change in frequency, the entrainment process may well start again. This has surely been tested though, I recommend searching Google Scholar with some terms like "auditory entrainment", "frequency" and "EEG", if you haven't already. Do you know how long the entrainment process takes? I can't imagine it's very long - less than 10 minutes, surely.
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