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There's several things that could be going wrong. On your Kindle under your Library check what your filter is set to. It may not be set to All and only books. If you've changed some of the settings in Calibre they will appear as Docs not Books. That might be why you're not seeing them until you search for them.
The other thing also, check that you are selecting Downloaded and not Cloud or All for the type of books. You may be looking at your Cloud and the books won't show up there because they've been side loaded.
The above options are usually what I see on my newer Kindles.
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