How did you reformat your sd cards? I have used sd association formatter in full over write mode getting good results. Other other formatting modes don't seem to work for kobo use. If you again have invisible book problem after loading new books it is caused by one of the books you just loaded. Past threads have explained how to fix such problem books. I just delete the problem book and look for the book from another source.
https://www.sdcard.org/downloads/formatter_3/