Well, thank you Amazon
for a very
sensible and logical methodology which builds upon the highly reasonable way you've been handling covers so far.
At least you wait until you're sure a new cover exists before deleting the old one...
So of course that workaround is slightly awkward
and I dearly hope you don't need to do this for a lot of books.
If you do... I wonder whether quiris' app would help:
https://github.com/quiris11/ExtractCoverThumbs/releases
It was originally meant for fixing books sent through the Kindle Personal Documents Service as dual-MOBI (so it downloads as AZW3 instead of old MOBI).
The app extracts covers from your books and creates thumbnails for them, it should serve as an alternative to calibre's cover sideloading altogether.
At the (time) cost of regenerating all thumbnails, it should automatically set the thumbnails from the books themselves, and unlike resending the book from calibre, it obviously doesn't touch the modification date of the *.azw3 -- so the Kindle should stop getting in a snit about the "official" covers.