In case of FOD, a fuselage puncture for example, what is the repair process? Considering time, complexity and cost, how is compared if it was an aluminium fuselage?
This is pretty broad and covers a wide range of techniques. But the airplane Structural Repair Manual (SRM) provides guidance, depending on the extent of the damage. Typically it involves excising the damaged or delaminated structure and patching the affected area. As with metal airframes, if the damage it too extensive the airframe may have to be written off as a total loss.