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Book View (BV) converts entities to their unicode equivalent character. This isn't something we can control as the third party component we use for BV does this on it's own. We do convert some characters to the entity. But we only convert ones that either can't be seen or are hard to differentiate (shy and nbsp for example).
Using the unicode character instead of the entity is perfectly valid. The entity is just a representation for the character.
As to why it only happens on some files, most likely it's because you didn't make a change in BV in some files. Simply viewing a file in BV won't change it. The code is only modified if you make a change in BV.
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