Finder treating symbolic links differently than terminal MacBook Pro Retina OS X 10.9.4
I was able to reproduce this as well (on OS X 10.9.4). A simpler case is as follows:

touch file.txt
ln -s file.txt link.txt
mv file.txt moved.txt
touch file.txt


If the Finder was open to the working directory while mv was executed, then it will (incorrectly) follow link.txt to moved.txt until it is restarted. Interestingly, you don't even need the Terminal to reproduce this bug, since it also applies to aliases:


Create file.txt.
Make an alias of file.txt.
Rename file.txt to moved.txt.
Create a new file also called file.txt.


The desired behaviour for aliases is to point to the moved file (moved.txt) unless a new file has been created in the original location (file.txt, created in Step 4). But the actual behaviour is just like in your example: Finder continues to follow the alias to the moved location until it is restarted.

This is a bug in the Finder. The workaround is to relaunch the Finder if an open window shows a symlink/alias while you move or rename the target file.