Ok, I copied the Calibre database to the Linux partition, and all the "wrong" books showed up during the database check
It's still a lot of work to fix this. And I learned my lesson to NOT change the title of a book in Calibre when not on a case sensitive OS...
If anyone has an idea to write back the book-title to the filename, or change the author temporarily and change it back to original, or another way to fix this quickly, please let me know.