Make sure you pop the SD card in the Switch first, if you can, and format it from there. That is the simplest solution.
Had you previously had a high-capacity microSDXC card in there before, or is this your first large card?
The Switch HAS to format SDXC cards before they will work. I think there is a non-Switch work-around, but I don't know what it is. If you can still boot into official FW, though, that would be the quickest and easiest method.