For CCU fares, this could just be the 'normal' CX practice for HKG-India fares. For tickets originating from HKG, CX just sells full fare Y to India, but does sell lower fare classes for the HKG-India sectors for tickets originating elsewhere.

All discount fares are booked via GC Nanda, a travel agent.

Been discussed here before - some say that the Nandas' lobbied on CX's behalf with the Indian bureacrats/government and the above arrangement was Nanda's reward/condition for that.
(well - it worked i think - CX win away a significant percentage of India-US West coast traffic that used to fly SQ)

Anyone got more juice on what exactly happened?

going very OT here:
One interesting tidbit that I heard was that the Nandas' proprietor used to be CX's GSA in India and for a long time continued to lobby against the opening up of HKG-India bilaterals for some vested interests (i have no clue...and make no claims to the veracity of the above!)

That said, I've been very happy with the service from these guys in HK. For the 20month period when i was commuting HKG-SIN pretty much every week, they knocked a decent bit off CX's published fares and were always prompt and on the ball with managing my bookings.