So tell calibre to stop.
Edit ==> Preferences ==> Integration with calibre (tab)
Uncheck "Update metadata embedded in the book when opening"
calibre embeds custom columns in the EPUB metadata during Send-to-device and Save-to-disk as well, it is meaningless to ask why it does so in the Editor specifically.
As theducks said -- it's stored so when you export the book, calibre can still retrieve the custom metadata if re-imported.
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