Originally Posted by thepossum
In other words, the problem was NOT that the Kobo database was corrupt. The problem must have been that the Kobo simply doesn't remove the database entries when html files are removed from the device.
So hopefully this relatively minor issue will be corrected with a future firmware update, and others having the same problem can be given a solution other than "wipe it and start over". ;-)
Yup. It's a bug. The kobo will process and add .html and .txt files to the sqlite database, but it doesn't remove them. I used an sqlite editor to clean mine up.