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The unzipping is not done by the ePub file itself, but by the software reading it. There's no reason that the software couldn't keep the TOC in memory after unzipping, but once the file is unzipped, it would be strange to delete the unzipped copy. They should be keeping the unzipped file in a temporary storage area somewhere, and reading from that.
Most people reading novels never use the TOC, I bet. They just start at the beginning, and keep reading until they are done.
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