If we make a pdf from InDesign CS 6 to the desktop and then make a change and try to resave with the same name we get a warning telling us that it cannot save because we file is in use. And then we cannot throw it out from the desktop.
Sounds like the O/S is somehow using that file. What do you have as the
default to open PDFs? If it's preview change it to Acrobat or Reader.
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