See the save() -7.3 option. You can save very large data structures when you use it. If you do not use it then by default you are limited to 2 gigabytes.
If you are getting anywhere close to 2 gigabytes of Huffman data then either you were working with long movies or you have a mistake in your implementation or your implementation is terribly inefficient.
The normal way to save Huffman data is to pack it into bit vectors. This is normally a nuisance to manage.
Fortunately if you use fwrite() you can specify a precision of the form 'ubitN' where N is the number of bits to write, such as 'ubit7' to write 7 bits. I have never used that myself though.
