User-Agent:       Mozilla/5.0 (X11; Linux x86_64; rv:6.0.2) Gecko/20100101 Firefox/6.0.2 Iceweasel/6.0.2
Build Identifier: Thunar 1.2.2

Thunar will overwrite symbolic links to directories rather than copying the files within the directories. This would be the expected outcome

I did this over a NFS mount, but I don't believe it should be a factor.

Reproducible: Always

Steps to Reproduce:
1.Create a symbolic link to a directory
2.make another directory somewhere else with the same name with some files in it.
3.move the files to the parent folder where the symbolic link resides
4. Thunar will ask you to overwrite it. If you do you will loose your symbolic link.
Actual Results:  
The removal of a symbolic link

Expected Results:  
Copying the files to the directory as if it was a real folder.

I consider loosing symbolic links loss of data when it deals with handling folder movement. I already lost data because of the behavior of it, in addition to the trash not working on some file systems. (no clue what causes that. likely a gnome-vfs error).