Having the same problem. Did anyone find a solution in which one didnt loose all the projects?
There’s no need to bother with Sysex. You can update easily with copying the other file (can’t remember the extension atm) on the CF card and reboot.
Done.
PS: always backup your projects before an update anyway… and even once a week 
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They say…
8.5.2 OS UPGRADE
Download the Octatrack OS file from the Elektron website.
Connect the Octatrack to a computer using a USB cable, select USB DISK MODE and press [YES] to make the Octatrack’s Compact Flash card appear as an external mass storage device in the computer.
Then place the OS file with the file extension .bin in the root (the top level of the file structure and not inside any folder) of the Compact Flash card.
Unmount the Octatrack from your computer operating system to exit USB DISK mode, select OS UPGRADE and then press [YES]. A prompt will appear asking if you want to continue with the OS upgrade. Press [YES] to upgrade the OS. Press [NO] to cancel the operation.
You can also use the MIDI UPGRADE option in the STARTUP menu to upgrade the Octatrack OS.
The active project will automatically be synced to the Compact Flash card before the OS is upgraded.
…in the manual.
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I’ll add disconnect USB before update (especially for mac users).
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