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Sigil's xhtml parser does not need or use entities. Instead, it converts those entities to their actual character value. That is fine for most entities except for whitespace ones so the CodeView editor highlights them with a red underscore so you know its there and working.
Adding numeric or named entities to the Sigil Preserve entities preferences will convert those characters back to their entities so you the editor user can see them.
But since you already have it in Preserve Entities, it should have kept the as entities.
Just run Mend All and your entities should re-appear.
I will look into why Generate Table of Contents is sometimes missing the Preserve Entities replacement step.
Thank you for your bug report.
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