The same thing happened to me recently on my Kobo Touch. Signing out of my Kobo account on the Touch solved the problem, but doing that does wipe all the Kobo-purchased ebooks from the device, which it then reloads when you sign back in. Took a while when I did it.
I'm fairly sure that annotations, notes and so on were retained when the books were reloaded. However, I'm sure this would only apply to ones made up to the most recent sync of the device. So, if you're going to try this, make sure you sync your reader first.
Oh, and I'm sure that the problem was not caused by failing to eject my reader properly when it was connected to the computer.