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It might not be related, but from my own experience and what I could read about the touch support in calibre. If for example you delete a book in calibre and add it back to it without first disconnecting, the book would not be detected, because they are still in the database. The Kobo will only clear it's database when it is opening.
You might see a expired tag in the device view in calibre which could hint at this.
Beside this small problem I never had any problem at all and I have mine since the first day. Adding around 300 books in 1 shot in calibre and no problem at all. I also don't see why the .calibre file would interfere at all since the have nothing to do with the kobo.
You might want to download a sqlite database viewer and check the sqlite file inside the .kobo directory, this file is the database and look if the books are really there after they have been processed.
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