If you are getting the error popup message from Windows that suggests that your Kobo either was not properly dismounted before the USB connection was made or that it was not safely ejected. I would not recommend trying to use Windows to fix it. Eject your Kobo and power cycle it.
The remainder of your symptoms suggest that your database is corrupted. The fastest way to fix this is to sign out and then sign back in. Again, I would suggest using NickelMenu with a menu item to reboot your Kobo before connecting it to your computer. See the
NickelMenu: An integrated launcher for Kobo eReaders for more information.
Where are you storing the books you are sending to your Kobo? Preferably in a directory in the root of the exposed storage? Are you using calibre or just dragging and dropping books from directories on your computer?
I've pasted a simple NickelMenu config file in the code box. Copy/paste it into a file and copy that file into the .adds/nm folder after installing Nickelmenu. The file name can be anything but I generally use nickmenu.txt.
Code:
# ------------------------------------------------------------------------------------------------- #
#
menu_item : main : Dark Mode : nickel_setting : toggle : dark_mode
#
menu_item : main : dropbox : nickel_open : library : dropbox
#
menu_item : main : Screenshots : nickel_setting : toggle : screenshots
menu_item : main : Import books : nickel_misc : rescan_books_full
menu_item : main : Toggle Auto USB : nickel_setting : toggle : auto_usb_gadget
menu_item : main : USB Connect : nickel_misc : force_usb_connection
##
menu_item : main : Reboot : power : reboot
menu_item : main : Shutdown : power : shutdown
#
# ------------------------------------------------------------------------------------------------- #
menu_item : reader : Dark Mode : nickel_setting : toggle : dark_mode
#
menu_item : reader : Reboot : power : reboot
# ------------------------------------------------------------------------------------------------- #
#
menu_item : library : Dark Mode : nickel_setting : toggle : dark_mode
#
menu_item : library : Screenshots : nickel_setting : toggle : screenshots
menu_item : library : USB Connect : nickel_misc : force_usb_connection
menu_item : library : Reboot : power : reboot
menu_item : library : Shutdown : power : shutdown
# ------------------------------------------------------------------------------------------------- #