I tried moving ".metadata.calibre" and ".driveinfo.calibre" to the parent folder. That didn't work. Also, centralized KO metadata breaks when you reorganize your library. I haven't tried myself but it's described in "About book metadata location.
Oh... I guess it's possible to edit those file and fix the paths. I think that's what you meant? I see that the files are json and each book has a "lpath" attribute.
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