At the moment if there are html comments in the text they have the potential to be removed. In Moodle sometimes we want to keep the comments to do things such as:

<div class='frog'><p><blockquote><!--[if !IE]><!-->Long text with tags that will<!--<![endif]--> be chopped off but <b>should be added back again</b></blockquote></p></div>

See MDL-51483 for how these sorts of comments are used.