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Each epub should have a unique identifier which is typically just the uuid on epub2 and on epub3 the date information is appended to the uuid to create a unique identifier.
The uuid is also used when obfuscating and unobfuscating embedded fonts that have not been subsetted.
Many e-readers ignore this value and generate their own unique identifier by hashing title, author, and date along with the epub provided uuid.
I would not worry too much about your repeating the uuid for books already published until there was some other reason to udate the epub.. I would though in the future use unique uuids for each epub version for those e-readers that cache or sort epubs by that uuid.
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