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Glad it worked out. In general books added to Kobo will show up in the I'm Reading section automatically when first installed and then are removed after the next sync or manage - just as you discovered. Somewhere in the user guide it explains this. It is to let you see all newly added books rather than have them 'buried' with all the rest when first installed.
The database is not really that complicated and, since it is just a file, you can copy it and "play" with the copy to see how it is structured. You can also replace it with a backup very easily if you mess up. As I mentioned, I had a book that did not show up in Calibre (never did figure out why) but was in the database and showed in my app - this was how I removed it from I'm reading. Having said that, if your not comfortable with playing witht he database then best to just leave it alone!
Enjoy your winter island reading by the wood stove!
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