I'm not knowledgeable about this, but my BookReader.sqlite is just 48 KB. I don't think that file is supposed to get as big as yours. According to:
https://www.mobileread.com/forums/sh...d.php?t=341536
davidfor said "BookReader.sqlite is largely used for some of the information related to Kobo Plus and library borrowing. I understand it gets used for other things, but, I don't know what they are. From my experience, it should be fairly small. I would only expect a large size like that if you are borrowing books from Kobo Plus...."
Based on that thread, I'll ask what the time stamp of your BookReader.sqlite file is and if you also have files like BookReader.sqlite-shm and BookReader.sqlite-wal?