closing a "nested" window with a button in PySimpleGUI and repeating this process

[Serafim]

As you use windows and not popups you have to catch signals from all windows.
Your code works with minor changes (I changed the "rc= reverseComplement(seq)" as I don't know what it does)

import PySimpleGUI as sg
 
sg.theme('DarkAmber')
 
layout = [[sg.Text('Reverse complement:', size=(15,1), key='-OUTPUT-')],
          [sg.Input(key='-IN-')],
          [sg.Button('Convert'), sg.Button('Exit'), sg.Button('Help')]]
 
window= sg.Window('Reverse Complement Converter', layout, finalize = True)
 
window_help = None
 
 
while True:
    win, event, values = sg.read_all_windows() # Read all signals from all windows
    if event in (sg.WIN_CLOSED, 'Exit', 'Cancel'):
        if win == window:
            break
        elif window_help and win == window_help:
            window_help.close()
            window_help = None
    elif event == 'Convert':
        seq=values['-IN-']
        rc= "YES!" #reverseComplement(seq)
        window['-OUTPUT-'].update(rc)   
    elif event == "Help":
        layout_help = [[sg.Text("This program requires a DNA sequence as an input and returns the reverse complement")],[sg.Button("Cancel")]]
        window_help = sg.Window("Help", layout_help, finalize = True)
         
window.close()