I had to do this once.  It was a PITA.  Client put a new engine in her Mercedes.  I'm pretty sure I had to calculate depreciation outside of the program and manually enter overrides each year.

From memory (which ain't what it used to be), if the expected life of the improvement is longer than the class life (5 years) it gets depreciated.  If it's less than the class life it's a repair.  I doubt this can be done via the Car and Truck Wks.  Luxury auto limits apply but I don't remember how I had to deal with a vehicle limited in year X and an improvement limited in year 1.  I just remember there were overrides involved each year until she finally sold it.