At least with effects like inflammation, caused by pro-inflammatory eating & living habits, it seems extremely plausible that your body gets harmed further when on such a lifestyle, and gets some "pause" from being harmed as bad during the time which are on a low-inflammatory lifestyle.
Problems with clogging arteries will get worse quicker when on the "bad" lifestyle than on the "good" lifestyle.
When you speak of "neutralizing" you seem to imply the reversibility of certain health deterioration, forward or backward. Many health issues seem only to get worse with progressing age. Worse slower or faster, but rarely better.
It seems that early stages of e.g. diabetes type II can be reversed by nutrition, though. Jack Challem writes about things like that in the book "Inflammation Syndrome". Sorry, no link to studies, but the book has many.
Let me just mention that on this topic, you will also find books written by not so scientific people. It needs some sorting.
As for studies, it may not be exactly what you asked for - showing that "bad" vs. "good" eating can cancel each other out.
But apparently, eating nothing, once in a while, alternated with "eating normally", can decrease some of the bad effects of the "normal eating"
Enter "Intermittent Fasting"