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I find the syncing with Reader for PC something less than desired. I had this issue in the past where I would created an updated epub, load it on the reader and nothing would happen. There was a time when uploading the new file would then replace the file with a new one.
I think your best option would be to ignore using Reader for PC syncing and just plug your reader in your pc and manually delete the old file off the reader and replace it with the new one.
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