Maybe then its more of a problem with TMO where the mods settings causes the game to wait (for something) instead of giving an upgrade; and you know its should be available, but the game dont want to give it to you. It's not like subs refitting is completely disabled (Balao still can get its '44 upgrade - cause there is nothing else available) its the time between patrols needed is all messed up - that is my theory
