Not sure if this is bug og feature request:
On midi track → Shift+Pad → Midi ports. These settings resetts on reboot. This should be stored in project.
Perhaps this might help you out. Go to the 9:03 min mark, you might have to save a midi map file to your SD card in order for it to bootup as you wish. Pt.8 - MIDI Only Tracks - Isla Instruments S2400 Video Manual
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