not sure why that would've caused that problem. the ctrNAND is separate from the sd card, so how it got messed up, I dunno. did you update to luma 10.2.1 while using the 256GB card? that would explain it.
I'm not exactly well-versed in 3DS CFW but that's all I did and nothing out of the ordinary besides changing from 64GB to 256GB so I thought it was worth mentioning regardless how insignificant it may be.
This New 2DS XL is pre-owned, bought it off online and it already came with CFW/LUMA 10.2, I didn't do much with it until a user on here mentioned to check if the device can be booted up without an SD card, if in the event the SD Card slot became damage or unable to read SD cards, then at the very least the New 2DS XL can be used/accessed without it.
Upon checking I was unable to boot up and it gave off a "firm patch 1" error. Did the same GodMode9 script and all's good.
Changed to 256GB was still on previous firmware running Luma 10.2, works fine until I updated the official firmware and that's when I updated Luma to 10.2.1, so it is:
1. Updated to official 3DS firmware via System Update (Wi-Fi). Cause I wanted to try the eShop and the only way is to update the firmware as I am aware Luma has also been updated to work with the new 3DS firmware.
2. After that I updated Luma to 10.2.1
Didn't bother to check without SD card if it will boot up until just now.