Function PointGraph.RemoveNode
void RemoveNode (
node  |         
Removes a node from the graph.
// Make sure we only modify the graph when all pathfinding threads are paused 
AstarPath.active.AddWorkItem(() => {
    // Find the node closest to some point
    var nearest = AstarPath.active.GetNearest(new Vector3(1, 2, 3));
    // Check if it is a PointNode
    if (nearest.node is PointNode pnode) {
        // Remove the node. Assuming it belongs to the first point graph in the scene
        AstarPath.active.data.pointGraph.RemoveNode(pnode);
    }
});
Note
For larger graphs, this operation can be slow, as it is linear in the number of nodes in the graph.