Communication between imx7d

What is the best way to transfer files (full-duplex mode) in bulk (some GB) between two iMX7D?

It depends what you consider “best”. The fastest way is probably is by using External Memory Bus. It gives you 16 bits data bus width on up 132MHz speed. But you need to build a special carrier board and do a some software modification.
The easiest way is by using Ethernet and some ready to use tools like nc or FTP or anything else.