I recently started to notice this as well. Each time I save a HTML code snippet in a code block and that HTML snippet contains a <br> tag it will get removed so the code snipped looks odd from what I had intended to paste in it.
After some testing and trying this and trying that I found that I could replace the <br> tag in the Evernote code block with a <br /> and this tag will not be removed in the Evernote code block. Additionally I can use the <br /> tag in my work and there doesn't seem to be any negative effects, at least so far.
I am far from being an accomplished HTML coder so a question for all of you seasoned HTML experts out there. Is there a down side to using an HTML <br /> tag? I mostly use the <br /> tag for CR/LF in paragraph block and in HTML email....