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The use of filename(n).ext names to avoid duplicates is a commonly used Windows convention.
On Windows there is no way that Calibre can create files named filename.doc and FileName.doc in the same location, Windows just won't allow it - period.
Like any application, calibre is subservient to the operating system in use. Calibre also has copious amounts of code to work with and around the vagaries of the different file systems it supports.
BR
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