I'm sure this was just random bad luck on my side, but here's what my sd card looked like after updating to latest kosmos, (while on 9.1 switch firmware) booting into the new hekate to take a look at the usb options (not actually clicking any of them, just exiting out of the menu again) and then trying to start cfw.
I got an atmosphere error "a fatal error occured when running atmosphere and titleID 010041544d530000"
and the option to reboot by powerbutton.
after that, more errors, when putting sd card into pc, no file system found.
and finally, after chkdisk /f, thats what my sd card looked like.
since hekate/nyx loaded just as it should right after updating all the files on sd card, whatever happened, likely happened while it was loaded or during cfw startup. (also, yes, it was fat32 formatted)
Gonna take forever to get all my stuff back together
___
so it seems to be a reoccuring issue with that sd card now.
i can reformat it, put the atmo files back on it, boot all the way to nyx, but eventually, the same error occurs and the filesystem gets shot again. its very weird... gonna try once more after a full reformat, but that's going to take a good while
the same files on a different sd card work...
_____
after lots of formatting and trying things out, I'm now almost sure it's not actually an issue with my sd card and this new hekate might just have an issue with large sized sd cards.
Opened an issue on their github. maybe if anyone else has a spare 400gb card to test if you make it into atmosphere using latest kosmos with hekate/nyx and so on?