I got around the worrying deletions problem by holding kmailtransport-akonadi, which got rid of the deletes. But then, I found, it hadn't solved the problem as I hadn't held akonadi and the kontact set up is now entirely blank. I have tried
sudo apt install akonadi-backend-mysql=4:22.12.3-2 akonadi-server=4:22.12.3-2
to get back the version replaced, but it's not available. Most unfortunate.
Perhaps I should unhold kmailtransport-akonadi, but that would leave even more to unwind if it's still broken.
I'd agree that anyone with Kontact/kmail should exert a little more caution at the moment.