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I have never had an issue with any of the Kindles in my family by plugging them into calibre. All calibre does is copy the books over with a special logic to also copy over cover thumbnails (and possibly an apnx for pseudo-random page numbers, unless you disable it). It shouldn't be any different from using the File Browser.
The Kobo on the other hand has a database which calibre edits -- maybe that is what messed up your Kobo? Although this doesn't usually happen (or we'd hear a lot more complaints, and calibre would stop doing it until there was a safe way to do so) sometimes things go wrong.
It sounds like more of a Kobo-specific problem in any event, rather than something which calibre does to readers in general, regardless of how repeatable the issue may be.
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