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Check in the (main GU) Metadata Editor: Formats section.
Do you have an Original_(xyz) listed?
This Tweak controls those:
ID: save_original_format (IIRC true is the default)
When calibre does a conversion from the same format to the same format, for example, from EPUB to EPUB, the original file is saved, so that in case the conversion is poor, you can tweak the settings and run it again. By setting this to False you can prevent calibre from saving the original file. Similarly, by setting save_original_format_when_polishing to False you can prevent calibre from saving the original file when polishing.
It is there to 'save you' if you did not have an external Original and you really messed up the Library copy.
I almost never use EPUB-> EPUB conversion, so I have it False and I also archive my real Original off system.
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