If the database which must live on the internal storage does not have enough space, you will run into issues.
If you are manually moving files from the .kobo/kepub directory, this will not work since the database will not have the new location.
If you are sideloading books, you might want to do a true factory reset (either manual or from the developer options menu) and use the external μSD card to store any sideloaded books.
Do you know where the space on your internal storage is being consumed?
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