This may have already been discussed in other threads but I would like to relate my experience.
I purchased my Kobo back in June from Borders Australia and purchased a few books via the desktop app.
Originally it had V1.0 firmware and when the V1.4 upgrade came along it went smoothly via the new Borders app V1.6
I have also used Calibre to side load some epubs and newspapers converted to epubs and also have used ADE to borrow library books.
A couple of days ago I thought I would check out the latest Kobo desktop app to see if it had the new firmware yet. (on another thread it was mentioned that Nov 22 was a "firm" date for the new firmware).
So, from the Kobo website I downloaded v1.7.5 of the Kobo desktop and created an account, downloaded a free ebook and synced the ereader to the desktop ok.
Then, however I found that the original Borders app (v1.6) came up with a message stating that it could not sync with the ereader. Also all the side loaded publications could not be opened anymore even though they could be seen in the I'm reading or books list.
Another funny side effect was that once a book was finished it still stayed in the I'm reading list marked as "new".
Anyway to cut a long story short I tried doing a factory reset but that did not help and I had to replace the database as outlined in one of the stickies and now everything seems back to normal.
Maybe it was just a glitch affecting my Kobo but I though others should know.