I have logged a job about this, but have been waiting for around 6 hours for an answer (and tomorrow is the weekend). So I am wondering if anyone has come across this problem before:
I uploaded spreadsheets in the back end of Treepl to move pages into folders in the Pages area. They look like they are in the folders in the back end. But two FTP programs (Dreamweaver and Filezilla) show the pages still in the Pages root directory and not in the folders I put them into. Why is this?
In the FTP if you go to “content” -> “pages” are the pages there as well? Are you sure they are not just in both places. I would just remove them from the root? 
EDIT: Sorry, have read it again. What if you reload in the FTP program, otherwise I would move them in the FTP. As long as you a backup of the files it shouldn’t be a problem
Hi Peter, thanks for your reply.
I tried that with a test file. It uploaded into the folder, but not with its template attached. And its file name had -1 added. So I would have to delete the virtual file, rename the actually-in-the-folder file and reallocate the right template to it.
This would be a huge redo of work I have been doing over the last two weeks on the site. It has around 2500 web pages and I was three quarters of the way through checking all links on the pages worked and the site menus linked to them OK. it when I found out about this problem.
I have been told by the Treepl team that they have found the issue causing the files to look like they are in a folder when in fact they are not. They said they would have a fix for it in 4 or 5 days. So I will wait and see what happens with this first I think.