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Hi. I can't see how using Calibre would cause any connection problems as all Calibre was doing was basically copying books over from the Calibre folder onto your Kindle which is a basic programming command. In other words, Calibre wouldn't be using any code to mess with your Kindle connection. I believe it was purely a coincedence.
I do use Calibre myself and transfer books over onto the Kindle. I've never had any issues.
If you are at all worried, just copy ebooks onto your Kindle manually. The Kindle should show up as an extra drive on your PC (usually f drive on mine) and you simply copy the books you want into the Kindle documents (correct me if I'm wrong) folder.
Amazon have to cover themselves but loads of people here use Calibre.
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