From what I've confirmed so far these are what affects if an enemy chases or flees from you
Confirmed:
- Number of people in your caravan (Including
prisoners, slaves, and escorted) - Weapons in your Primary slot
- Strength of the enemy (Their numbers and weapons)
- Monetary value of weapons
Doesn't affect:
- Items in Inventory
- Armor
- Tough reputation
- Weapon in Secondary slot
- Animals