[tomsem]

If you have Books filter set, you will not see any of your send to kindle books.

For side loaded books, you should make sure they are marked as 'personal document' (CDEType=PDOC) and not 'Book' (CDEType=EBOK). KFX Output plugin does this by default (as of a recent update). This also enables cover thumbnails to be generated for side-loaded books on the 2024 (or prior model) Kindles. Calibre will generate and side load thumbnails, regardless of CDEType, but that's not possible with the 2024 models. (And those thumbnails can get removed, requiring re-connection to calibre to restore them)

If you are side loading AZW3 then my understanding is that it requires some 3rd party metadata editor to change the CDEType to 'PDOC' (if it is not already thus). I just checked and it seems calibre sets it to EBOK by default when converting to AZW3.

Perhaps that is why the removal is happening. (as others point out if ASIN matches amazon book you have not purchased it can get removed - but I think only if it is marked EBOK).

I've never been able to reproduce this problem.