That sounds as if either the database is corrupted though calibre should give you a message about that or the internal µSD card has exceeded it's write lifespan and is not in a read-only state.
If you have Kobo Utilities installed with calibre, you can use it's database check function otherwise, you can use pretty much any SQLite tool. Copy the KoboReader.sqlite database to your computer and run the database check on that file. I'm using SQLite Expert Personal since I was used to it from a couple of projects at work but there are several options. You can try copying the entire exposed partition to a directory on your computer and using Kobo Utilities to save the reading status (Store/restore reading positions => Store). After that, you can try the following in order:
- Sign out to replace the database with a blank one (More => Accounts => Signout). This does not remove your sideloaded books and they will be imported but reading positions will be lost.
- Factory reset to wipe the exposed partition but leaves the firmware alone. More => Settings => Device information => Factory reset your eReader. All your sideloaded books will be removed and will need to be restored from calibre.
- This one assumes that you have done a search for devmodeon to enable Developer mode. Once that is done, More => Settings => Device Information => Developer options => Factory reset your eReader. This will wipe the user partition and restore the firmware to the factory firmware. As in variant 2, you will need to restore any sideloaded ebooks. Any patches and add-ons will be wiped. This is equivalent to the manual factory reset.
After any of these procedures, you can restore the reading positions using the Restore option in Kobo Utilities Store/restore reading positions.
Alternative is to copy the files/directories you copied back to your Kobo and doing a restart.
If the read-only state is the case, you can try removing the µSD card, creating an image and writing the image to a new µSD card. See the the
Memory Upgrade Mod Guide (With Pictures) thread for some help with this.