Jacob seed was the first family member I killed. I went through all the cut scenes, fight stages, etc, and remember watching him slump over against the rock. I played the rest of the game as normal and eventually killed the other two (Faith and John) only to find Jacob Seed isn't dead when I check his region on the map.Faith and John are registered as dead on the region map.
I've gone back into Jacob's region and tried running around, completing stray missions, fast travelling to the Wolf's den, trying to enter his compound, etc. None of it seems to change anything and I can't encounter him anymore which makes sense since I killed him. However, I can't get the game to give me credit for it. The weird thing is that the Wolf's Den is completely empty of NPC's - not sure if that happens when you kill Jacob or not.
I'm not sure what to do at this point but am welcome to any suggestions. Really hoping to not start over completely since I've logged so many hours already.