When my brother installed Publii on his computer (MAC OS X) and changed the Sites location to a directory in Dropbox he got a warning that the everything in the directory would be removed. Thankfully that didn’t happen because we had already put the new website in this directory. The fact that it didn’t remove the directory could be a bug? Having said that: is it really necessary to remove all the files/directories in the new sites directory?
I made a backup of the website before configuring Publii on his computer so the website was never in real danger of becoming lost.