This is not possible on an Octatrack. The MIDI upgrade option is simply for just that, OT firmware upgrades and nothing else.

The only Sysex anything the OT does are parameter changes on the MIDI tracks, even those actually may be CC commands.

As for backing up the OT itself, just simply connect it by USB to a computer or connect the compact flash card direct to computer (card reader needed) and copy the set folder that is on the card.

Ultimately you will need a computer for the back ups and the C6 software may not be pretty but it will take sysex dumps from any standard MIDI instrument.