I'm using client side drag and drop, and no templates, just some HTML in the text field. I have a ton of code to deal with different scenarios that is wholly uninteresting to you. What I've found is that as soon as you enter the onClientNodeDropping event, if you check eventArgs.get_sourceNode().get_text(), any HTML tags are completely gone. Also gone were some 's I had added.
I have a workaround in place at the moment that fixes the whole problem. I save the text in a custom attribute (called "Text"), and use set_text after each drag and drop. Just thought I'd bring this up because it's very weird.