In my case, I made the change on my hard drive (cut/pasted about 200 folders/files from one path in my working copy to another path in my working copy), and used SourceTree (2.0.20.1) to stage both the detected changes (one add, one remove), and as long as I staged both the add and remove together, it automatically combined into a single change with a pink R icon (rename I assume).
I did notice that because I had such a large number of changes at once, SourceTree was a little slow detecting all the changes, so some of my staged files look like just adds (green plus) or just deletes (red minus), but I kept refreshing the file status and kept staging new changes as they eventually popped up, and after a few minutes, the whole list was perfect and ready for commit.
I verified that the history is present, as long as when I look for history, I check the "Follow renamed files" option.