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I see calibre's custom metadata in opf files all the time. Sigil doesn't delete it that I know of. Perhaps you're confusing not being able to add/edit (or even see) those custom entries in Sigil's metadata editor with "removal" or deletion? Check the opf file... I think you'll find the custom entries are still there.
If it's syntactically correct (for epub2), Sigil leaves it alone as far as I know. But if it's not in Sigil's defined list of items... all adding/deleting/editing of any such metadata will have to be done by manually editing the opf file.
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