This looks like a bug with the class names changing like that. But I've seen things that sort of look like bugs with css normalization actually not be bugs in the past.
Was the div with class="center" in your original code, or is this created where Calibre split the files?
Also were there any settings in extra css, or was that empty?
Smallcaps isn't really supported in the epub spec, so there is a small possibility there is also some special casing code coming into play here.
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