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The fact that the second epub had the proper file structure but all files were full of NULL 00 bytes may indicate your ssd/harddisk is corrupted. If you have the equivalent of fdisk (like on linux) or DiskUtility (like on macOS), it can at least check and fix missing sectors/data on the disk.
That might be worth a shot as well. And once the disk is repaired try looking in Temp again.
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