This is most likely a limitation of the description being stored in an xml file's attribute value:
<attribute id="Description" value="This is my mod description" type="30" />
Really what we need is the description to be stored like this:
<attribute id="Description" type="30">
<![CDATA[
[h1]My Mod[/h1]
[list]
[*] I am using Steam Workshop markdown.
[*] [b]Isn't it great?[/b]
[/list]
More description text
[url=nexusmods.com]Nexus Page[/url]
]]>
</attribute>
CDATA allows every character after it to be taken literally - perfect for adding line breaks and markdown. With it, we could store our complete workshop description in the editor, and not have it constantly replace the description with every upload (even a blank description overwrites what's on the workshop).
A way to disable the description would be nice - So we could keep what we added on the actual workshop page and not have the editor's version overwrite anything.