Then look on your PC if the Files are present.
If they are it's most likely a broken Micro SD Card Connector / Reader.
Hekate runs before the Switch Firmware...
libsys_lp0.bso is in the files. And so is libsys_minerva.bso.
How can I find out if it has to do with the sd card slot?
Inject the Hekate Payload if you face any 1-Bit Mode Error it's the Reader.
In Hekate go to Console Info -> micro SD and look for Errors
If you have access to the ipl File try to boot into Stock Mode.
Or Disable Auto RCM and burn your Fuses to boot into Stock Mode.
You don't need a working Card Reader for the Switch to run.
You're supposed to use the Spare SD for testing, since you don't know if the other is Corrupted.
Atmosphere & Hekate are less than 20 MB to Copy, how does it take long?
Then you either operate your System without CFW & SD Card or you have to replace either the
Card Reader itself or you need to resolder a new 16 Pin FPC Connector.
Just don't use any force when you click it in or you might break it completely.
And don't send it to Nintendo if you want to repair it, go to some local Phone Repair Shop
or you will get a patched Unit in return.
emuMMC should not have any effect on the ability for SD cards to be read.There's one more thing I'm wondering, just to know in case it's not the hardware, but is it possible for something done with or on the emunand side that could affect both it and the system files in a way that system would have trouble reading or processing micro-sd cards? (including in booting hekate)
I can try replacing the card reader (in time), but before doing that I'd like to rule out the software side.