The box could have had 1299 flying hours when fitted, no reason to assume it was a new or zeroed box, simply a serviceable part which was fitted to replace a gearbox which needed to come off. It could easily have come from another machine undergoing some other sort of heavy maintenance.
I'm also confused by the idea that specific authorisation is needed to carry out standard maintenance such as changing a gearbox, to get extensions yes, but I would not expect to see any external requests to comply with routine procedure.