Your decision to transfer the property to your son and be entitled for permanent residency as his descendant is the right one in your case. Regarding the already three years passed, they are counted to the seven years needed for the citizenship application.
How can I apply for Greek citizenship?
I’ve been holding a resident permit as a real estate owner of Greece for three years. Since my son is turning 24, I want to transfer the property to him and reapply for another resident permit as his dependent. Do the years I spent holding my first permit count toward the years of residency needed for a citizenship application? Or do the years start counting after I obtain the second permit?
Yes, all years count . But you must be able to prove that it was actual residency, which is not always the case with the permit of residency since you have no obligation to actually live in Greece in order to be entitled to keep your permit of residency.
All years count but need to have no gap between the permits. Nevertheless, having the permit of residence is neither a condition to get citizenship nor does it give a certainty that you will receive citizenship.