For backuping books bought on the kobo store, I use the calibre obok plugin from the noDRM/DeDRM_tools github repository.
Calibre:
https://calibre-ebook.com/
On windows, install the Kobo Desktop App from the kobo website. (I don’t know if obok can be used on mac, and no kobo app on linux
)
Connect your account used to buy the books.
As the obok plugin is accessing the database of the kobo app, I never have the kobo app and calibre launched at the same time.
Download the books within the kobo app (don’t worry where they are stored).
Close the kobo app.
Launch calibre.
With the obok plugin installed, you should have an "Obok DeDRM" button in the top toolbar.
It will show a list of the books downloaded with the kobo app.
Select and import them.
Once it done, close calibre (after importing books with obok, my list of books is always buggy and need to restart calibre to work).
You can now launch the kobo app again and remove the books downloaded if you want.
You can use calibre as your library, or export the books as epub files from it if you want.