According to a recent article, one user found that his file contents were changed after sync. I repeated the expiriment with an HTML file and found it unchanged. However, I don't doubt that in some circumstances this could happen. I've seen lots of changes to files uploaded to SharePoint, generally related to SharePoint Designer.
The question is, why would this happen? If we don't know the cause, I wonder if there are repeatable cases of this or if there are flaws in the article author's methods.