I had a quick play and it seems the article is all good now. Having the old MyArticle\ appear is annoying. This most likely happened because of some bad data our end.
Some more background: initially all articles simply referred to downloads in their MyArticle directory without any recording in our database of what was actually in that directory. We fixed this by scanning the directories and recording, and associated, downloads for files.
In some cases we had servers that were out of sync and so this association was inaccurate. When this happens the submission wizard doesn't know how to trim links because it doesn't trust anything other than what the database says.
That error will be triggered anytime a major portion of the template exists in the content.
With the new submission wizard you don't need to publish it to save it. You can hit the Save Draft button and your current work will be saved as a draft. To view drafts, just go to the submission page[^] and you'll see, on the right hand side, your drafts.