If someone's father passed away, who makes the brocha of baruch shepotrani when he gets his aliya at the torah by his bar mitzva?
Shaare Chayim, a commentary by R. Chayim Tz'vi Ehrenreich on Shaare Efrayim, says (4:24, in my own, loose translation):
I saw in… [???], writing in the name of Maase Ish responsum 14, that one does not say this blessing for his orphaned grandson whom he is rearing. Now, that book is not at hand, and it seems to me to require further investigation; after all, don't we hold (Shulchan Aruch, YD 245:3) that he's obliged to teach his grandson Torah? And then obviously if he didn't teach him appropriately he's punished. So it's very fitting to say "Blessed is who freed me" according to one explanation in Magen Avraham (225:5, q.v.)…. I found this also in the book Ir Mivtzar on maseches M'gila: that he had suggested precisely this to… the Maharsham of Berzan and he replied briefly, "according to our practice that we say 'shep'tarani' without mentioning the Name or kingship, it's appropriate that his grandfather say it".
The source for this minhag is from the Medrash (Bereishis Rabba Toldos 63:10) and Achronim also bring it from the Maharil (SA OC 225:2, the Rema there and others).
The Magen Avrohom (Sif Katan 5 there) says the reason for this Minhag is that until now, the father is held responsible for the son's Aveiros and with the son becoming an adult according to the Torah, the father is exempt from this point forward. If the father is no longer alive, he is already exempt from all punishment and logic would indicate that the Brocha is not made at all. According to the Levush as brought by this Magen Avrohom, the Brocha is exempting the son from punishment he might receive because of the father. The Chochmas Shlomo there has a long piece discussing this approach.
Nevertheless, here too, if the father was Niftar already, it seems logical that the son was already exempted and again the Brocha is not necessary.