Thanks for helping !
I'm not very familiar with all this FW stuff but I'm keen to learn. So I've been reading other discussions and I am not sure I understood everything correctly so I'll try to resume.
The MidiBoot (or bootloader) is what makes magus visible as a midi device via usb connection. Some incorrect firmware can disable it because the bootloader isn't able to reset itself. Then the only way to load a FW is to use a programer to flash FW with SWD connectors.
If FW flash is successful, I'll have the bootloader set as it was before and my device behaving exactly as it was before with the same FW.
Then there is this thing about updating the bootloader so that it can reset itself. It is not yet a stable feature (why?). But as long as you have a programer and you are ok to remove the digi board everytime you want to reflash you're fine.
Now I am not sure how you flash with SWD. I saw a video where you use this st-link utility to flash .hex or .bin files to your device (using program and verify). How do I get these FW files ?
Another thing worth mentioning is that the midi command did not work last time I tried with magus. I have some data overflow issues which I did not know how to fix. So flashing FW the old way could be a solution for that if I decide I do some FW hacking.