Yes,one has to pay.Any gain or loss when you are not selling the shares is purely notional and will not be taken into account for calculating taxable income.The fact is that you have sold the shares and have incurred gain on those.And as the shares were with you for only six months,the gain on sale will be short term capital gain and tax has to be paid thereon,the market value of other shares may have gone down in this period,that does not matter.You can take that into account only if you sell the other shares also at that low price and actually incur loss.
