Here's the deal. A refit is a cursory procedure of just taking on fuel and torpedoes. Maybe minor fixes could be done. Fixing leaky fuel tanks is not one of them. In order to do that you would have to drain the tanks and most likely take the sub out of the water. That only happens when you end your patrol.
By refitting and going back out you are cheating yourself. The only time certain types of damage, like hull damage and fuel tanks, are fixed is between cruises. Not only that but between cruises are when ALL equipment upgrades are granted. At that time only, the blind chimpanzee tosses his darts at the new equipment board and if his dart hits that radar upgrade, you have the chance to install it. Running around in 1944 with 1941 equipment is a sure way to failure and mutiny.
There is no reason for any refit unless you elect to stop by Midway on the way home for a quick splash of fuel and some torpedoes in case you run into a Japanese merchie where he doesn't belong. Actually before I leaned to manage fuel well, I used to stop by Midway on the way out instead.
The most efficient way to run your sub is to stay out for the minimum amount of time necessary to accept two or three missions or run out of torpedoes. Then return to base and end the cruise. That is not a bug or defect in the game.
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