It seems like you are writing over the same label. Its probably updating, but to fast for you to see.
Try using a timer instead of a while statement.
or something like this:
extends Panel
var i = 0.0
func _ready():
set_process(true)
func _process(delta):
if i < 1000:
i += 1 * delta
get_node("Label").set_text(str(int(i)))
else:
get_node("Label").set_text("Done")