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Are those the exactly same file (i.e: md5sum or sha256sum produce the same hash)
If not the sync server won't work and the result you got came from your 2nd book sync (1st page) while your 1st book progress was never synced.
If you use calibre to push books to your devices please double check because, by default, calibre stores some settings inside epubs making those different books for the sync server
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