The only issues I am aware of are chapter detection and multi-file HTML.
For chapter detection:
Quote:
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The default is to consider <h1> or <h2> tags that contain the words “chapter”,”book”,”section” or “part” as chapter titles as well as any tags that have class=”chapter”.
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Or you can use whatever you like for chapter detection by overriding this, as illustrated by gwynevans. Calibre will then automatically build a TOC for you and add page breaks before each chapter.
For a multi-file HTML ebook I think it is still the case that you need a root HTML file that references the rest (e.g. a TOC file). So it may be easiest to produce the original as a single HTML file.