This could be a software issue but for me this behavior (on a v1 Switch atmosphere emunand) was a prelude to my SD card losing the ability to write altogether. (i.e. it wore out its writes and locked itself) Now I don't use emunand anymore and have had no issues.
For my OG switch using the old RCM method, I agree, I've had no issues on R58. But it runs on emunand as well