Wanting to right his ancestors wrongdoings during the slave-trade era, a youngboy struggles to attain peace as he unwittingly rekindles an age long war.

After unwittingly rekindling an ancient war, a youngboys survival depends on him stopping the war at all cost even if it means coming up against his ancestors wishes.

Rekindling the war is your inciting incident, correct? It's what sets the story in motion? If so I would put that first. That will help separate the two instances of war in your logline and help eliminate the confusion.
'After rekindling an ancient war..."

Do you know HOW the protagonist restarts the war? Depending on what the HOW is that may be important enough to include.

JanCabal

Things to note. Maybe this will shed more light into helping me get a great logline....

There is an older world living in parallel with this world as we know it in which there "is" a bitter war

The war "froze" in the older world over time but actions of good intent, to make up for injustices of his ancestors, by youngboy in todays world will, unknown to him, "unfreeze" the older world, causing the war to continue....

Sole victim of the youngboys ancestor (from the older world) crosses into the world and wants to claim what belongs to her but now in youngboys custody.

Youngboys health is ailing and he thinks by doing the "right thing" he will be okay