Moving desktop folder back to where it should be! I've had a real headscratcher... the other day I was downloading a large folder from FTP to a folder on my desktop. When I went to check the files half were missing, I soon found out it was because they were in a different "Desktop" folder. Basically at some point of downloading something moved my actual desktop folder from my /Users/Username/ folder to /Users/Username/.tsclient/

All the files on my desktop are as they should be as whenever it was moved OSX kept an eye on it and still uses it. In my user folder there is a desktop folder with the other files that were missing from that FTP download I did. 

To make matter even more confusing, if I click Desktop in the left hand favourites in Finder it takes me to the /.tsclient/ folder, but any apps that pull up a finder dialog for the purposes of loading/saving point to the on that is in my user folder, where the desktop should be.

I didn't accidentally drag and drop my desktop folder into this folder (as .tsclient is hidden), I never type in an admin password for something if it pops up without exact knowledge of why it's there, and I wasn't doing anything out of the ordinary so I have no clue why and how it moved. But it has, and I want to move it back!

I can't seem to delete or rename the one in my user folder, if I could I can't seem to move my desktop folder back out of that folder, it only wants to copy it. I guess I could move it using terminal but I have no idea what's going on and don't want to mess things up even more!

Does anyone have any experience of this bug or how to remedy it?
Having a bit of trouble following your description of the situation. It'd be helpful if you used actual path names instead of "The one in my user folder" type descriptions.  

You have a backup right? Ok then...

The sidebar link is just a shortcut, so it doesn't really mean anything by itself.  Fix that last. Just delete it and then re-add it.

Run a disk check and permission repair if you haven't already.  

If ~/Desktop doesn't exist and you're sure it was some how renamed .tsclient, use terminal to move/rename it back. I think its more likely that your ftp client uses that as a temp location and that the files there are only partially downloaded though.  

If ~/Desktop does exist then just move the folder contents back where they belong not the folder itself. Then delete and re-add to the sidebar