In my view it is not possible. Because the MB64 project and the MB16E project require a discrete core-module with a separate pic-firmware. but of course you can integrate both projekts in one case
…the rotary encoders circuit ( http://www.ucapps.de/howtoenc/rotary_encoder_ciruit.gif ) is designed to work with the MIDIO128 - maybe i’m wrong but i think that the currend MB64-firmware do not work with relative midi messages and rotary encoders.
In the MIDIbox64 firmware a lot of tasks are running in parallel (Pot driver, Display driver, Button/LED Driver, Bankstick Driver, MIDI Handler).
The sampling period for the buttons is only about 10 mS - thats not fast enough to detect the transitions (falling and rising pulse edges) which are sent by the encoder.
The MIDIO128 firmware is optimized for digital IO, the sampling period is about 1 mS and works better, but in my oppinion it’s much easier and more fail-save to use a second PIC, running with MIDIbox16E firmware, because the required adaption circuit for each encoder is complex and expensive.
Or wait for MIDIbox NG - it will scan up to 128 digital inputs like MIDIO128 and will come with a built-in encoder driver, so that every single input can either be assigned to a button or to an encoder (every encoder requires 2 digital inputs…).