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In the old days you just fired up iBooks and deleted it from your Library shelf. Then exited out of iBooks. Then fired up iBooks and manually added the new version of the epub.
If in the new Books app that no longer works, then I would open Calibre or Sigil to edit the epub's opf and change the unique id pointed to in the opf package tag with a newly generated uuid.
This would/should force a new cache entry.
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