pwd in bash is wrong after sending directory to trash
This behavior actually has nothing to do with the .Trash directory.  You can get into a similar situation by moving your current working directory to any other location.  The pwd command and echo $PWD will both be inaccurate. 

What I have found is that starting a new bash process will correctly identify the new location of your current working directory.  Therefore a workaround would be to simply "refresh" your current bash process with a new one with the command exec bash.