https://www.sdcard.org/consumers/formatter_3/
At above link Download SD Card Formatter and install it on your Windows or Mac computer
Open the SD Card Formatter it should find the and list the SD Card you have attached to your computer.
I give the card a name, My Books.
Follow these steps.
Format Option: click on "Option Button"
FORMAT TYPE: Select "Full (OverWrite)"
FORMAT SIZE ADJUSTMENT: select "OFF"
Click on: "OK" Button
Click on: "Format" Button
Full overwrite formatting is painting over the old graffiti making it blank so Kobo can't read old writings and is available for writing new books or data.
Quick formatting just sets flags in disc index indicating "disc blocks contain no data and available for new data. The old data is still there to be over written with new data or restored.
Kobo Linux is Ignoring the deleted index flags, restores the index and data then tries to use the corrupted database to display books.