I’ve done the quest and chosen my powers but i dont get rep when i kill the sundered flame.
You don’t get rep for merely killing NPCs.
The rep comes from random drops that may be awarded when you loot them.
Farming Cobalt Assembly reputation is simple: Just kill Sundered Flame enemies in the area. They have a high chance of dropping Wild Arcana which will increase your Cobalt Assembly reputation. Uncommon Moderate Arcana grants 15 Cobalt Assembly Reputation, while Rare Major Arcana grants 45 Cobalt Assembly Reputation.
Since the drop of Wild Arcana is random, you could go several kills without seeing any rep increase, or you could get a string of rep bumps for a number of kills in a row.