You should probably be using a stream to read your data in and another to write it out. If you are gong to need access to data later on in the file, save it. If you need access to something you haven't ran into yet, you need a two-pass system where you run through once and store the "stuff you'll need for the second pass, then run through again".
Compilers work this way.
The only case for loading in the entire array at once is if you have to repeatedly randomly access many locations throughout the array. If this is the case, I suggest you load it into multiple byte arrays all stored in a single container class.
The container class would have an array of byte arrays, but from outside all the accesses would seem contiguous. You would just ask for byte 49874329128714391837 and your class would divide your Long by the size of each byte array to calculate which array to access, then use the remainder to determine the byte.
It could also have methods to store and retrieve "Chunks" that could span byte-array boundaries that would require creating a temporary copy--but the cost of creating a few temporary arrays would be more than made up for by the fact that you don't have a locked 2gb space allocated which I think could just destroy your performance.
Edit: ps. If you really need the random access and can't use streams then implementing a containing class is a Very Good Idea. It will let you change the implementation on the fly from a single byte array to a group of byte arrays to a file-based system without any change to the rest of your code.