According to me in your case Long Term Capital Gain arising from sale of Nifty Linked Debentures is taxable in your hand, since what is exempt u/s 10(38) are Long Term Capital Gain arising from transfer of Long Term Capital Asset being an equity share in a company or a unit of equity oriented fund, where the transaction is chargeable to Securities transaction Tax.
Since in your case its Nifty linked Debenture so the Long term capital gain arising from its transfer is taxable and accordingly you can set off your Short term Capital Loss arising from sale of equity shares against long term capital gain arising from sale of nifty linked debentures.