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Rebooting does not force indexing...
No, calibre conversion does not render the book unsearchable. What renders the book unsearchable is if the book contains images instead of proper text, but I doubt that is the case.
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If the indexing claims to have suddenly completed after a reboot, I would be inclined to think it somehow got tricked into thinking the book is indexed when it actually isn't.
Try deleting the book from your Kindle, then plugging it into the computer and resending it from calibre. Then wait for the indexing to complete normally (it indexes in the background, so there is no sure way to know when it is done -- but it gets a more favorable priority when charging).
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