We cross posted. Yes removing those lines and the index.txt file and removing any files by those names inside the epub, is the right direction. Or just use the .epub file you posted to start new.
It almost looks like a virus or some computer based php indexing program is injecting these files into the temporary folder used by Sigil. Maybe a whole computer indexing program, or a bad anti-virus program, or a virus itself.
If so, you should find what program generates those files and shut it down asap.
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