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 (B) by not only the foods patients eat but also by when the patients eat them (C) not only by the foods patients eat but also by time when the foods are eaten (D) by not only the foods that are eaten by patients but also by the times the foods are eaten (E) not only by what patients eat but also by when they eat it
There is no problem in A, but E is better, since ETS prefer parallel structure. "What patients eat" is a noun clause which can be treated as a noun, and it is not a complete sentence. "It" can refer to this noun clause.