As ASER indicated in his last reply, time life for the shafts (MGB Shaft, Main Rotor 3G6320A01852 and MGB Shaft, Main Rotor 3G6320A01853) are 16000 hours and 54000 landings.
With regard to which is used - total sortie hours or winch time:
If you break the formula down, FT + (2.5 x winch cyles)
You will note that the actual penalty is 2.5 x winch cycles, which is
added to the total flight time for that sortie. (remember, the total flight time would have counted toward timelife anyway, you are just adding the penalty).
Hope this clarifies the hours counted...