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ePub readers do "pre-parse" the whole of a flow when that flow is loaded into memory. What they don't do is to pre-parse a different flow that you might jump to (eg a separate flow containing an endnote), because they don't have enough RAM to store a parse-tree for the entire book in memory. It's up to you, as an ebook creator, to ensure that an endnote is contained within the same flow as its reference if you want good performance.
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