Hmm for me it works as expected, it looks like I really did not understand you.
from panda3d.core import NodePath
from direct.showbase.ShowBase import ShowBase
class MyApp(ShowBase):
def __init__(self):
ShowBase.__init__(self)
all_node = NodePath('all')
for i in range(0, 10):
for j in range(0, 10):
model = loader.load_model("panda")
model.clear_model_nodes()
model.set_pos(i*10, j*10, 0)
model.reparent_to(all_node)
all_node.flatten_strong()
all_node.reparent_to(render)
print(all_node.ls())
app = MyApp()
app.run()