The log mentions "Charis SIL Compact", "Charis SIL Modified" and "Charis SIL SmCp Modified". And it seems to be reducing their size. The first one is the one you are embedding now. Are the other two already in the books?
Or maybe they are just in the conversion options. If these books were converted before using the other fonts, those settings will be saved and reused. You could reset the conversion options for these books of them and see if the font references go away.
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