Assuming you have main data and new data

mainData = existing_Points
newData = generated_Points
tolarance = 1
tree = KDTree(mainData)
indices = tree.query_ball_point(newData, tolerance)
unique_indices = np.unique(np.concatenate(indices))
if len(unique_indices) == 0:
   print("No intersection found")
else:
   print("intersection found")

Is this what you need?