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Spellchecking should now handle soft hyphens without barfing. Search and replace will not unless you use regex to deal with them. Another way to just see the soft hyphens is to add the soft hyphen entity (named or numeric as appropriate to your epub version) to Sigil's PreserveEntities setting.
That said, I urge you to remove the soft hyphens for general work. You can add them back after the book is polished and in near final form using calibre if you really want them.
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