If you stay submerged long enough to see an CO2 icon appear in the upper right hand corner of the screen, you need to surface by clicking on the icon. The boat will ventilate. I never had a CO2 problem by doing this.
As for the damage not being repaired, are you sure you were not still in "Silent Running"? The only other thing I could think of is that mabey the damage although slight, was of the nature that could not be repaired at sea.
