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Hmm scratching my head a bit here - over the weekend I reconnected the USB pcb and core pcb and was able to upload the seq v4 project.hex file successfully.
I just finished the JA pcb and went to upload the ng_v1_036 project.hex file for testing, but MIOS studio doesn't seem to recognize my core at all. MIOS Studio does see MIDI IN/MIDI OUT named MIDIBox SEQ V4+ (and the other 3 seq channels), but no response from the core.
Troubleshooting steps so far:
Removed SD card PCB from c