It feels like a pretty big plot hole/oversight imo. When we used him to fuel the tower, the way he talked about the act of using him as fuel, was that this was a finite thing. It was a sacrifice on his part, and that his soul would be destroyed for good.

It seems you might be right though, from the journal entry of Hope Upon a Flower:
Perhaps inspired by an impossible memory of you in that ancient time and place, Elidibus suggests that you travel to Elpis in the past. At his instruction, you open a pathway to your destination, and step into the portal. The magick consumes Elidibus's essence once and for all, and he goes to join his beloved brethren as you journey to your distant destination in search of salvation.
That last line seems to really contradict itself though, if it consumes his essence once and for all, how can he join his brethern? Ha.