You are supposed to confirm that the converted EPUB did
not go horribly wrong, and then delete it. The one and only reason for the ORIGINAL_EPUB to exist is so the conversion itself doesn't wipe out the input file.
Kovid has stated his views on the matter -- that if your new EPUB is good enough to sideload and convert from, then you have no need for the ORIGINAL_EPUB anymore. calibre doesn't care about it, and calibre doesn't want to care about it. YOu have already agreed that the new version is good.
P.S. An ORIGINAL_EPUB would only be created if you did an EPUB-to_EPUB conversion, or Polish Book, not when you open the editor.
Polish does not typically cause massive changes that need to be reverted, and if you edit the book, then why would you also convert it to itself?