There are a few things (in latest version, 188.8.131.52) that don't really survive round-trip from markdown back to markdown:
- reference-style links (e.g. `[foo][f]`). They are converted to inline links e.g. `[foo](http://...)`.
- setext vs hashmark headers. `foo\n=====` will get converted to `# foo`.
- markdown allows for forced-linebreak <br>s to be added with two trailing blank spaces at the end of a line. Pandoc escapes these with a trailing `\` at the end of the line.
These are only occasional nuisances, but overall the documents (at least in my experience) are not butchered.
I also occasionally go from markdown to docx for the purposes of uploading to google-docs and copy/pasting large sections into other docs. This is the only markdown-to-google-docs workflow I've found that works to preserve formatting. It's never really butchered anything, except a few times the syntax-highlighting for code-blocks gets confused and keywords get the wrong colors.
You can choose whether reference links go at the end of the paragraph or the document.