Just because he is having his name in khatha or pahani does not mean that he is the owner of the land.
You have the following options:
a) if your name is mentioned as buyer in the sale deed, then based on the sale deed, you can apply to taluka office for mutation of khatha and pahani in your name. It will not cost you much in terms of time (provided you take care of officials) and money. Here you will get your names included in khatha and pahani. That way you are keeping the ownership records clean with the government agencies and ensuring no hanky panky stuff by your nephew or his children. In this option there is no physical partition of properties, only your ownership details are updated in government records.
b) Second alternative will be to effect a partition(through court) between you and your nephew . The partition will by metes and bounds. this way both of your properties will be demarcated, marked and physically partitioned and the same will be registered in sub-registrar office and taluka office. . The advantage of second alternative is that not only you end getting your name in government records, you also end up any disputes with your nephew as the properties are now separated, physically demarcated and both of your properties are well defined and mutated in government records accordingly.
Hope this helps.