I think the best thing for you to do is to draw the whole window again, removing the pop up. So when the condition to send the message is met, redraw the window with the message, and then after a few seconds, redraw it again without that pop up. The window is redrawn all the time when your screen refreshes anyway, so you're not doing anything drastic.
I am doing notification window and I want to do when massage pop up is shows for some time and then it clears it self.
I know how to do that it waits with time.sleep() but I dont know how to clear screen.blip().
How to clear screan.blit()