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i suspect that amazon systems apps are auto-managing the books that you bought from amazon i.e. they are moving any such detected books to the " correct" folder. and maybe removing them to match amazon's record of what is cloud only and what is also on device
but amazon shoudl not mess with sideloaded books, unless it is doing some match on ASIN
as for folders. FYI on my own tablet [ fire HDX] i just downloaded a recent book from my cloud to see where it goes.
it does not go into the books folder, not into the obvious kindle folder either [ storage emulated 0 kindle is an empty folder]-books downloaded direct from amazon go to android...data... com.amazon.kindle... files.... and most are further obscured by the KFX format
but when I use CC to sideload azw it is configured to place those in the books folder and they then appear as books on the device. Actually I rarely do that, instead I convert to epub and put them into downloads cc folder, to read with moon+.
moving on - you say that both AZW and Mobi are prone to vanishing - what about epubs- not opened by the kindle app but read in a 3rd party reader app ?
you could - as yet another detective process / magic trick , add some epubs via calibre + CC ,put them in your downloads folder and see if you can make those vanish by any combination of actions. use whatever reader app for epub that you have to hand, or just download a free one to test with
as for deleted vs moved: try this. send one book like before via CC, and use file explorer to confirm that you at first see a book file in the expected folder, and note the file name. Now make it vanish, then use file explorer to search all tablet folders for that file name, or even for all files with today's date to check if it has moved or gone
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