This was ridiculous. I have 4 different adapters at home (for microSD cards) and only 1 of them was read by 3DS (and it was not the one that originaly came with that microSD card but the one from my smart phone). I am formating now.
Edit1: emunand tool not responding at 60% while injecting the nand back to SD card :/ I try to wait some more. Not responding and cannot be shot down even from processes menu :/
Edit2: I had to pull the card out from PC and then the program disappeared. Trying injecting again now and hoping the data will not be corupted somehow.
Edit3: Injecting complete. Copying the data from old SD card back and then will try it. Wish me luck!
Edit4: It seems working
Edit1: emunand tool not responding at 60% while injecting the nand back to SD card :/ I try to wait some more. Not responding and cannot be shot down even from processes menu :/
Edit2: I had to pull the card out from PC and then the program disappeared. Trying injecting again now and hoping the data will not be corupted somehow.
Edit3: Injecting complete. Copying the data from old SD card back and then will try it. Wish me luck!
Edit4: It seems working