Never seen anything like that before. I can't get Sigil to mess up the original either. If Sigil did it, then we don't have the whole picture.
But first let me take a stab and guess that you pasted your html into Book View?
When I paste your original code into an empty Book View tab (as plain text), I get this back out:
Code:
<head>
<title></title>
</head>
<body>
<p><head></p>
<p><meta content="text/css" http-equiv="Content-Style-Type"/></p>
<p><title>Jennifer’s Magic: Book 1 — Vigilante</title></p>
<p><meta content="version 1.6.1" name="description"/></p>
<p><meta content="Cocoa HTML Writer" name="Generator"/></p>
<p><meta content="1038.36" name="CocoaVersion"/></p>
<p><link href="../Styles/styles.css" rel="stylesheet" type="text/css"/></p>
<p></head></p>
</body>
Which is eerily similar to your result.
Granted, you don't have all the entities in yours, but the metadata is certainly being moved out of the head and into the body and the title emptied. Perhaps you cleaned up the entities a bit first?