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The only way this can happen is if the longer path is too long for windows, which will causes calibre to be unable to read that file. When that happens, calibre will look for files of the same format in the directory and use the first one it finds, automatically copying it to the correct filename.
You shoudl be able to fix it by simply renaming the author/title to something short and then naming it back.
There was a bug in the pre 1.0 version of calibre that could end up creating files that were too long for windows in some corner cases, that bug has now been fixed.
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