Try deleting all the files that are invisible to the Kindle, and re-adding them a couple at a time.
The indexer can sometimes jam on a bad file, and refuse to find any more.
Once the bad file is removed, the Kindle will start seeing them again.
Adding a couple books at a time helps you narrow down which file is bad.
To sideload that one, you will have to reconvert it in calibre -- that usually fixes it.
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