[Tkinter] _tkinter.TclError: can't invoke "destroy" command: application has been destroyed

[Yoriz]

In the line

toplevel_windows.after(3000, toplevel_windows.destroy())

you have called the destroy method by using () so it happens imediatly, the result of the method is what is then called by after
remove the () so after makes the call itself.

toplevel_windows.after(3000, toplevel_windows.destroy)

P.S. I don't know why you have mainloop calls everywhere you should only have the one mainloop call, the mainloop call before the after call is probably blocking so that when the window is destroyed and you call destroy the window is already destroyed.