Dave,
Instead of “interlinked” I think you mean “Ethernet connected”. The InterLink accessory can only connect two units together and cannot work with the i-Pilo Link of the Terrova trolling motor.
I would disconnect each unit from any accessories, update the software and power them off. Next I would reconnect the accessories to each unit and turn the units back on but only one at a time and would shut each unit down after it comes up and recognizes the accessories it is connected to. After all have been updated this way I would power all three on at the same time.
Are you also going to update the software in the i-Pilot Link and/or its remote?