Swiss as a bootloader on the Wiikey Fusion can be implemented as two different methods:
Skip the IPL, boot directly to Swiss (custom "apploader").
Appear as a disc in the IPL just like the current menu.
Currently, I've written (ported from the official flasher) some code to do the flashing and it seems to work well as it's giving me back valid responses but I believe the file I'm flashing may be in the wrong format (layout).
This is what I've done so far:
I took a known "flash" file and injected my own DOL into it. I then flashed the entire file. The IPL with the wiikey was telling me "Please insert a GC disc" and the Wiikey was generally unresponsive. Luckily the next time I tried to flash, the recovery kicked in and took over, resulting in a working chip again (or I could've just run the official updater again).
What I'm pretty sure I actually did and why it didn't work as I expected (silly late night coding is to blame
I flashed the entire 2mb flash file to the section where "firmware" related updates are meant to sit (not the ISO file, but the actual low-level firmware that drives read commands/etc). I'll try again tonight when I get a chance, pretty sure that was my issue though and trying it tonight should hopefully give some good results!