If you have experienced an error on your Kobo and it will either not start and/or your library of books has disappeared, you have nothing to worry about, in most cases.
First, you can try a soft reset by holding down the power button until it resets, then try syncing again. You may have to hold down the button for several seconds. A reset in this manner should require no further action on your part other than resyncing the device to your computer.
If this doesn’t work, you should be able to reset the device completely and then download all of your purchases by re-registering the device using your existing account. If it hasn’t completely reset, you can do that by one of the following methods:
You can reset to factory from the Home screen by going into Menu > Settings > Advanced > Reset Device Now
If you cannot get into the menus, then you can achieve the same thing by pressing and holding volume up while turning the device on with the power button. It will confirm that you want to erase data, so confirm that and then continue.
Then just set up as if the unit were brand new, using your existing Kobo account information. Once this is done and the Kobo is online, it will sync your existing library from your account.