It is to do with your original text needing to be Markdown.
Hopefully this will work here, but you need to add two spaces at the end of a line to indicate a new line rather than a line wrap.
Example Note title
first line of the drafts body
the second line
some
other
lines
with a gap in between…
From the spec. at Daring Fireball.
When you do want to insert a
<br />break tag using Markdown, you end a line with two or more spaces, then type return.Yes, this takes a tad more effort to create a
<br />, but a simplistic “every line break is a<br />” rule wouldn’t work for Markdown. Markdown’s email-style blockquoting and multi-paragraph list items work best — and look better — when you format them with hard breaks.
The end result for me in the HTML then looked to be much more like what I imagine you expected to be passing to Evernote.
Hope that helps.