> So it is ok if I don't follow the recommendation in this case?
That seems like a subjective call to make, and it certainly isn't mine to make -- given that the question is neither about how scores are calculated (they are calculated using the "improved algorithm" regardless) nor to Inquisit more broadly. If you can put forth good arguments for not excluding subjects, I'd say it's fine. But I am neither in a position to find those arguments (I know nothing about your broader study) nor to judge their merit (my opinion matters little; what matters are the opinions of your co-authors, reviewers, thesis advisors, etc.).
Hope this helps.