Fifty-five?

[Nimrod's Son]

He's in some other part of the building alive and encounters Xykon on his way out.

He's in some other part of the building dead and Fyron doesn't know it yet and Xykon for some reason doesn't rub it in his face(possibly not knowing that it was Fyron's son).

Eugene's set-up for the story makes it unlikely the son was in the building at all. He arrived with a takeaway meal for the two of them (as he apparently often did) to find Fyron and Xykon mid-standoff, and as he entered he was calling his master's name, not any others.

This just after a montage of scenes throughout Eugene's time with Fyron, too, with narration talking of the father-son relationship they had. If Fyron already HAD a son, that would rather complicate matters, or else they would all be one happy family. I can't believe that Eugene and Fyron could be that close and yet the son's death doesn't warrant a mention.

i don't recall the exact reasons why Xykon killed Fyron(its late here dun wanna think) but it's possible that if Fyron was hunted down by Xykon, it's not too much of a stretch that he ran into his son at some point.

There was no hunting down. Xykon took a tour of Fyron's museum, saw a crown that he thought looked totally badass, and returned that night to steal it. He didn't even necessarily intend to kill its owner; he just wanted the crown.