When a U-boat returned from patrol it was scraped and repainted while the crew was on leave and the u-boat was in dock, simple as that
Read the book "Black May". In it there are excerpts from captured U-boat men who were imprisoned with members of the other branches of the German armed services. This was done to extract information that was not possible from interrogations. For instance a planesman would be put in a cell with a captured luft pilot. They would share stories and information and all the while the room was tapped with hidden mics to pick up the information.
The pictures you see of rusty U-boats are of those that have been at sea for several weeks and endured the elements. 10 weeks at sea will do that to any ship. Uboats did not leave port looking like rusted out hulks.
