When i try to overwrite an amended existing pdf file via export I get
>> file already exists. Do you want to replace it?
>> ;'Cannot save to the file, because it is already open.'
This occurs even after Reader closed down.
Only way I could resolve is by closing down and reopening Indesign.
This happens when the reader is open in the background.
If you are using windows check with Task manager > Process
if Mac than check Activity manager.
End the reader process from these places and see.
Arthursever said that he had shut Reader down and was still getting the message.
If this is so, you should try restoring your InDesign preferences.