I'm not sure how to fix it best/fastest.
What I did, once upon a time, was to create a new library in Linux, on a case sensitive file system, and *import* all the formats from the case insensitive Windows file system. First made sure the metadata was fully updated for all books. And I imported with setting one book per folder.
Then I used my Linux library as the main library. That was the only place where I ever edited metadata and added/deleted/converted books. And I copied (really synced using rsync) this main library to other filesystem only as backups and/or for read only access. Now I don't use Windows anymore, so I don't have problems of this type anymore. Good riddance...
I don't think there is a problem with FreeFileSync. The problem is you trying to sync between filesystems with different case sensitivity, in the wrong direction... If you copy/sync correctly named files from a case sensitive file system to a case insensitive filesystem, then I think you are fine, but not the other way around.
But I suggest that you still test carefully!
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