area_trade_trader was indeed the issue. I checked their behaviours and copies these values from defend_job to trader_job;

scene_toughness_threshold = hardest
flee_scene_threat_style = hardest
loot_flee_threshold = hardest

Now traders do not instantly run away from fights(I think) but run when their hull drop down to 75%. But I get to keep trader NPCs without them retreating all the time. Thanks guys!

There is a cascading load order.
That means that nebula, asteroids and encounterparameters always belong to the top of the file since the stuff loaded below requires these entries being in memory at the point of processing.

The order does not matter. Nebula can be above or below Asteroids… you can even mix it. The only important thing to remember is that zones and objects have to be below.