No it's not lost because you've bought it from Amazon, therefore it'll still be in the cloud.
It doesn't matter how you get the book you've bought from Amazon onto your Kindle (delivered wirelessly, emailed to your Kindle, downloaded to your PC and sideloaded using USB), you've bought it from Amazon so it's stored in the cloud.
[edit: too slow., so just to echo what HarryT said!]
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