Vindicta's Assassinate damage is measured first. If it is not lethal, the added damage from separately tracked items are counted instead and Vindicta (and her team) will not receive bonus souls. Relevant items include:
Mystic Burst (+35 damage)
Quicksilver Reload (+65 damage)
Improved Burst (+9% target's Max Health as damage)
Escalating Exposure (+6% Spirit Amp per stack up to +120% amplified damage)
Mystic Reverb (+40% damage after 3 seconds)
Effects that add the Spirit stat or reduce the target's resistance are not separately tracked, so that damage is instead credited to Assassinate...
