Try using p7zip as your zip manager. its free and ad free as well. Sounds like either your decompression tool is eliminating duplicate file names or possibly a virus/malware scanner is interfering. That file is the same name as the one in the vn folder but they are not the same file size. I'm only guessing here. Without actually watching the decompression operation, there isn't a way to verify this.
FurryClaws696
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A member registered Aug 24, 2022
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You should add the Linux icon next to the windows icon for the PC version, and include Linux as a supported OS. Renpy already generated the .sh file which is for Linux. Otherwise Linux users might not consider checking out your VN thinking it wasn't supported. You might also need to update your manifest file for the itch.io page so the itchio app will recognize the linux file. I can assure you, the VN runs fine in Linux since that's my OS of choice.