I recommend to avoid using old c style arrays in c++ in favor of only std::vector (or std::array for static sized arrays).
Your adjacency list could be implemented using:
std::vector<std::vector<int>> adj(N);
This is using the std::vector constructor that accepts a size, and enables N to be dynamic (whereas in your code it must be known at compile time because c++ does not support VLAs - variable length arrays).
Cloning is easy:
std::vector<std::vector<int>> clone = adj;
If you must use a c style array, you can clone it with:
vector<int> clone[N]; 
std::copy(std::begin(adj), std::end(adj), std::begin(clone));
A side note: better to avoid using namespace std - see here Why is "using namespace std;" considered bad practice?.