You can add a custom column where you can manually set a book to whether it's been read or not in calibre.
1. Open Preferences
2. Click on "Add your own columns" (at the top of the preferences page)
3. Click on "Add custom colum" at the bottom of that window
4. Define a lookup name e.g read
5. Define a column heading e.g Read
6. Choose yes/no as column type
7. Click Ok on that page
8. Click Apply on the page you come back to
9. Restart (close and start it again) Calibre
Now you should be able to mark books with a yes or now in the column read.
You can either click on the field of the column that belongs to the boo in the book view and choose the state or you click on "Edit metadata" with the book marked and change it under the "custom metadata" tab.
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