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Unfortunately, I think the end result is going to be a factory reset to solve this. But, I do have some ideas and questions.
After the power off and the book isn't show properly, have you connected and looked for the book in the device? Has the book been removed?
Have you tried calibre? I think you will get an error with the database, but that will gives some extra information. Alternatively, any tool that will read an SQLite database.
What happens if you let the device sleep rather than powering off? If the books don't get lost, then that is a workaround until you are ready to do a reset.
Is the file system OK? If it isn't, Windows will normally ask to check for errors when you connect the device. If you are asked, then do it.
If a factory reset is needed, you might be able to save the annotations and highlight. I've done this once for one book, but haven't needed to do it for a lot of books.
On the device, there is a directory called "Digital Editions". Within this are two directories. "Annotations" is the one you want. Within that is are files with the extension "annot". These contain the annotations for your books. Or at least the epubs. Each epub will have a file in there with the same name as the epub plus the extension "annot". If our epub is in a subdirectory off the root of the device, then the annot file will be in a sub directory of the "Annotations" directory. So, the contents of "Annotations" is a replica of the contents of the device (excluding the ".kepub" directory).
What I have done once when doing a factory reset, was to copy the annot file to my PC. After the factory reset and putting the epub back onto the device, and letting the device process the epub, I put the annot file back. When I opened the epub again, the annotations and highlights were all back.
As I said, I have done this once for one epub. When doing it, I made sure all the names (directories and files) were the same.
Also, the annotations/highlights are also stored in a database on the device. Before trying the above, I tried saving the rows from this and putting them back. That didn't work and the rows disappeared when I started the device again.
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