I tried following the guide for setting up Publii on a second machine to edit an existing site. When I point Publii at my site folder on Dropbox it tells me that it is going to clear the destination folder. I don’t want it to do that, am I doing something wrong?
I misunderstood your question. You have to choose the same directory. If the folder of the second machine is empty, there shouldn’t be any problems. If you backup your DropBox Folder before changing the folder on the second machine, nothing can go wrong. You have a backup.