Too curious, had to check.
I'm using the first sd_uhs module I uploaded yesterday. (based on older automatic version of Danne's sd_uhs module, no pauzes no messages on screen)
Now go into Canon menu, select format card, keep ML.
And go

Ok, works, card got formatted, ML got restored and camera restarts and behaves normal, can record raw video with ~80Mb/s.
So the automatic version without pauzes and messages seems safe to have enabled while formatting card in cam.
Although A1ex did mention somewhere, that during the patching process, there must be absolutely no card access, otherwise you could end up with card corruption.
So Danne is probably right that it went bad during formatting and using patch 2 on the 5d3
