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And I was able to track down the issue for Sigil on macOS and Linux. When reading in a manifest item, it looks at the href for a ":" which should only exist in the url's scheme and if it exists, the href is considered to be external and not actually present in the epub. Using external resources in the manifest is allowed in some case under epub3.
So all and all a very strange beast set up to fail on almost very platform.
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