Did you make sure the epub's stylesheet worked in ANY reading system? There has been no recent changes in Sigil that would cause any reading software to ignore valid, and properly linked stylesheets.
Moon+ Reader's entire reason for being, however, is predicated on allowing users to ignore/override an epub's integral styling. I suggest you begin your research in Moon+ Reader's users preferences (or the Moon+ Reader user forum) before assuming Sigil is the reason for your recent woes.
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