Yeah, most serious editors do syntax highlighting and other fancy stuff. Trying to do that on an 8MB file is asking for trouble.
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It's not about saving space. If anything, the combined total will be slightly larger because of duplicating the <head>...</head> content -- although standard EPUB compression will nullify that.
It is about handling each logical chunk of text in easily-digestible bites.
You can still use regular expressions on all the XHTML files in the book. The Editor's Search & Replace tool allows you to select the scope of files to affect.
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Have you seen Pablo's quick and dirty
EPub Tutorial?