operator error is always the most likely cause of such things.
when i first got calibre years ago i set it up to process ebooks for my kindle. i would add small batches of books and always tediously enter metadata which is when i glommed onto the title modifications which are now causing me headaches. and back then i didn't even connect the kindle as i had another brain fart scheme to add each book from caliber via the 'send to kindle' function which would keep a copy in the amazon cloud for me and those copies would always be available to the kindle from anywhere i was. this all worked well for many years, but i sure didn't use caliber for much.
i think the problem crept in when i started experimenting with moving the calibre library around to various devices and cloud storage so i could access my books from devices other than the kindle. anyway, that's the only way i can explain it unless i had a hare-brained clean-up scheme and somehow managed to blitz all the metadata entries from within calibre itself and didn't notice.
i plead very guilty to not ever understanding how metadata worked. up until a few days ago i thought my calibre metadata entries were going back into the actual epub and mobi files although, considering the kindle didn't always show what i'd entered into calibre, i should have figured things out quicker. but, with most of us, our goal is to read, not to tweak. and i'm paying the price now--i've restored the metadata on 500 of my books and have about 2200 to go.
btw, i was very disappointed in that /polish/ function i discovered along the way. it only applies to epub, not mobi which is the format which would go onto my kindle. it also promises to put a metadata page into the epub file, but doing a /view/ from calibre doesn't show one on any of the books i tested. but since it doesn't operate on mobi files, it's not that useful for my current situation. i get the idea it's more for epub authors and i suspect i'll come back to it if i have occasion to upload something else to kdp.
/guy