PM sent. But...
Try a factory reset using the last set of instructions on
https://wiki.mobileread.com/wiki/Kobo_Reset:_Glo_HD. That could trigger a correct update. It probably won't, but, it's worth trying.
And consider getting a new SD card. This can be a sign that the card is starting to fail. You can safely use a larger card and expand the books partition to use it all.