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Are you running KSM on the device? There was a bug in one version of that which caused problem like you describe. The last version solved this.
Otherwise, you can try closing calibre and ejecting the device using the OS functions and seeing if that helps.
What OS is this happening with?
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1 - I don't know what 'KSM' is. As far as I am aware, the only software on my device is the software produced by Kobo. It automatically updates, so whatever the current version of that is, I have it.
2 - As I usually only use the Kobo with Calibre, I've never tried ejecting from Finder; I will do that from now on and see if it ejects properly when Calibre can't.
3 - I assume you mean computer software here? Mac OS 10.13.6
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The backup is a zip file containing the database plus a few other files. The restore is simply unzipping the file and copying the database to the device replacing the one that is there. Then eject the device and restart it.
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As the backup file is a .sqlite, not a .zip, I can't simply open it & copy/paste as directed. How do I open it? I tried an online viewer (see attachment), and none of the files were a database file. Since I couldn't extract them, it wasn't useful anyway.
As for the error messages, I get a different one every time I try to do something; doesn't seem to matter which order I do anything, I just get error messages.