Hi!
According to this topic here, it looks like Navio2 have no support of rotary encoders at all.
I can offer you really straight forward solution: you can utilize some sort of microcontroller, that will collect encoder data for you (e.g. Arduino) and you can pass that data over some interface (either I2C or UART). On Raspberry, you can create ROS node that will collect encoder data from the chosen interface and calculate odometry data.
Although I do not really understand the part about relaying it back to Ardupilot. I’m not sure that there is a way…