Unless there's another translation error in my Seafall copy, you shouldn't be able to do the same action twice in one turn. The repair action says "Repair a ship..." not "Repair all ships..."
So there's no way of repairing both ships in the first place.
In the English rulebook, page 15, about the Builder's Guild:
2. Repair OR Upgrade
(Upgrades costs gold and can be discounted with a good, ship must be present)You may either repair both your ships or upgrade one of your ships.