[chaley]

I don't see this behavior.

My experiment:

1. Look at the db with SQLiteSpy. Find a float custom column. Image is below.
   
2. Change a value in calibre, in this case 9.01 becomes 9.02
3. Look at the db again. The value has changed and there is no duplicated row.
   

What are you doing that is different?

I also note that the table has a UNIQUE constraint on the book_id, so the db itself should toss exceptions in the case you describe.

CREATE TABLE custom_column_16(
                    id    INTEGER PRIMARY KEY AUTOINCREMENT,
                    book  INTEGER,
                    value REAL NOT NULL ,
                    UNIQUE(book));

CREATE INDEX custom_column_16_idx ON custom_column_16 (book);

CREATE TRIGGER fkc_insert_custom_column_16
                        BEFORE INSERT ON custom_column_16
                        BEGIN
                            SELECT CASE
                                WHEN (SELECT id from books WHERE id=NEW.book) IS NULL
                                THEN RAISE(ABORT, 'Foreign key violation: book not in books')
                            END;
                        END;

CREATE TRIGGER fkc_update_custom_column_16
                        BEFORE UPDATE OF book ON custom_column_16
                        BEGIN
                            SELECT CASE
                                WHEN (SELECT id from books WHERE id=NEW.book) IS NULL
                                THEN RAISE(ABORT, 'Foreign key violation: book not in books')
                            END;
                        END;