The chance of an upgrade when ending a patrol is a random roll of cyberdice. However editing the unit parts configuration files for each sub to remove the overlap in tower availability dates is supposed to help. Each conning tower is available for the entire war so even if you are successful in a roll and could get an upgrade it might be negated by recieving the same tower you already have. Edit all those files to end the tower interval the day before the new one is available and you might just recieve one on your next career.
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