Updating officially will burn fuses and prevent you from downgrading to lower firmwares without using a bootloader in RCM to bypass the fuse check (and even if you do, the console cannot go into Sleep Mode). So you won't be able to utilize exploits on lower firmwares and any CFW that don't support 6.2 (hence why I mentioned that Atmosphere is the only CFW that supports 6.2 currently since there is no ETA on when other CFW will get support)
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Not all homebrew appears to be supported on firmware 6.2 despite the exploit giving us access to all firmwares. Some examples of currently unsupported homebrew on 6.2 include kezplez-nx (for dumping keys) and gcdumptool/WAIN cart dumper (for dumping cartridges). And as more and more firmwares come out, more and more stuff will break (which can be fixed but fixes take time).
Most likely your console initially had exFAT support for the firmware it was running, but when you updated, you didn't choose exFAT so exFAT support wasn't applied to the firmware you were installing. Also did you use ChoiDujour or ChoiDujourNX? Don't tell me it doesn't make a difference as these are two completely different applications used on two completely separate systems.
I'm going to try converting a my exFAT sd card into a FAT32 to see if that will do anything.