You could always try with a fresh post to avoid breaking anything on your site. Besides, wordpress has a history of changes you can revert to.
What I did was copy the entire functions.php file in my theme (some 1000 lines of PHP and HTML) and added it in the HTML view. I then switched to Visual and back and did a diff. All that was modified were the spacing between the text and the Crayon tag. The contents of the pre tag containing the code were kept intact.
What WILL break the code is if you start inserting < and > (angular brackets) unencoded into the code. This is not valid HTML! You must encode these as & lt; and & gt; so it doesn't get picked up as HTML tags itself. The decode:true option in Crayon then decodes them back into <>.
Note that the Tag Editor automatically encodes and decodes the brackets you entered into the dialog correctly - it's only when you forget and add an unencoded bracket outside the dialog that it can break. It's best to use the visual editor when possible :)