Dental caries and gingivitis can be exacerbated not only by the foods patients eat but also by when the patients eat them.
(A) not only by the foods patients eat but also by when the patients eat them
(E) not only by what patients eat but also by when they eat it
A and E both use " by when", so it shouldn't be a reason to rule out A.
Also in A, "them" unambiguously refers to "foods".
But in E, there is no reference to "it", which might be "the food". how can a pronoun refers to a noun that doesn't appear on the sentence?
Why E is correct but A is not?
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