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I have changed CC to make the scan-on-connect ignore files that differ from books in CC's database only in case. This will fix the problem you are having and similar problems, such as when an author or title changes only in letter case.
I am not totally convinced that I am not creating new problems. For example, on some Android devices the file path "author-Title" really is different from "Author-Title". If on such a device a user puts a book differing only in letter case into the library folder then connects as a wireless device, with this change CC will ignore the book. My guess is that case changes in tags, titles, and authors are far more common than wanting a new book to appear from a scan with a letter-case difference. We will see ...
BTW: my guess is that you got into this situation because metadata download fetched tags differing in letter case from what was in your DB. If you accept the download then calibre will change the case for all books with that tag.
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