Then I don't know what your problem is. As a matter of troubleshooting, I would do the following:
- Remove all CFW files/folders from your SD card (that would be folders like /sept/ and /atmosphere/)
- Download the latest Atmosphere
- Download the latest fusee-primary (next to Atmosphere)
- Download these signature patches (for Atmosphere v0.13.0)
- Put Atmosphere and the signature patches onto your SD card
- Put the SD into your Switch
- Enter RCM
- Launch Atmosphere using fusee-primary
After performing these steps, is the SD card recognized?
In short, Nintendo's exFAT drivers on the Switch are poorly made, and they increase the likelihood of corruption, whether or not one is even using CFW. This is an issue that affects OFW, Atmosphere, ReiNX, SX OS, etc.
I've been driving for fourteen years and have never been in an accident. That doesn't mean it won't happen, and it doesn't mean I shouldn't wear a seatbelt.
It is highly recommended that you switch to FAT32, although it might not solve this particular problem.