I mean absolutely no disrespect here but if I read your initial post correctly you are using third-party software that is known to cause issues and you are going to return your Kobo? I can't see how this entitles someone to a refund - if I use aftermarket tools or modifications on my car then the warranty is void. If I load a third-party OS on my phone then the warranty is void. If I use third-party tools to modify the data on my Wii then the warranty is void. Ect, etc. I can't say that I agree with the reasoning behind your wanting to return the unit.
Now before anyone gets all crazy about this statement a quick search of my username will out me as one of the guys who was tearing apart the Kobo SQLite DB to see how it ticked. I do use Calibre, I have modified the SQLite database on my Kobo by hand on several occasions, and I do do things to the Kobo that are well beyond what it was intended for. However, if the unit freaks out and starts eating my books I know full well that it was my fault for messing around with it in the first place.
As a result of all my poking and prodding I have found that simply loading my ePubs onto my Kobo via Windows Explorer to be the most effective and error-free way to get them on there. Calibre is a great tool but I don't trust it to mess with the DB yet.
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