Changing p-value adjustment method during major revising
I'm sure you already know this because you have been working with it in your manuscript, but the Benjamini Hochberg procedure is for avoiding false discoveries. So, in other words, Benjamini Hochberg is, I'm sure you know, a procedure you use to reduce Type I errors, where you incorrectly reject true null hypotheses, which are false positives results.

If, upon revising,you discovered "many spurious results that very subtle change are considered significant," it sounds to me as though you may, possibly, have considered some of the results in your latest draft to be false positives, prompting you to change your statistical procedure to Bonferroni for your next draft.

The key point to keep in mind here is that Benjamini Hochberg avoids false positives but Bonferroni tends to produce false negatives.

Therefore, the real question is why your switching statistical procedures. If your hypotheses, your work, and  your  data all indicate that the results are trending toward false positives, then Bonferroni is the way to go.  Otherwise, switching procedures at this point may not be, in my own opinion, the optimal way to proceed.