These are two different things :
One holding period is of the property which you have sold i.e the one on which capital gains are being calculated . There is amendment in this holding period. Property being sold which was held for more than 2 years will be taxable as long term capital gains.
To get these capital gains exempt , you have to invest in different kinds of properties mentioned as per those exemption sections. If you transfer the new property you have purchased before 3 years then your exemption is withdrawn and your exempted capital gains become taxable.So there is mandatory 3 year holding period of new property . You are mixing up this holding period with the one mentioned in first para. There is no amendment in this 3 year holding period.
Hope its clear now.