The error in calibre means the database on the device is corrupt. The device will seem to be working, but it is running on an in memory copy of the database. It is unlikely to be able to write changes to the database and if you power off and on, it will lose any updates such as the reading positions or recently added books. If you don't have a backup of the database, the fix is to sign out of the Kobo account. This will replace the database with an empty one and load the books after prompting you to login. If this doesn't fix things, you might need to do a factory reset.
The light not going off is unrelated. A recent firmware change means that the light doesn't always get turned off when the PC is connected to the PC.
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