The settings of concern for you are the i2c bus addresse’s because that’s where the zynthian looks to see the encoders it expects. The all in one circuit provides another set of encoders but it is presented to the i2c bys in the same way as the zynscreen so I’m pretty sure the addresses will both be 0x20 which will confuse the bus and also the zynthian.
The solution is pretty simple thou’if you have chips in sockets on the allinone. Remove the 23017 chip ! It doesn’t contribute to the MIDI implementation so it all should work as you want.
If the chip is soldered in then another method would be to change the addressing on the allinone to point at a different address. There are three address pins A0,A1,A2 setting any of these to the opposite logic state with careful and judicious use of a soldering iron and pliars. If you don’t mind a certain amount of mid air work you can cut the pin above the board bend up the remaining stub and solder that , with a small piece of wire to the opposite poliarity. You shouldn’t need to do anything more than this as the chip will have an address just simply one you don’t use.