Your persistent Python path is usually set via a shell startup file like ~/.bashrc.
Modifying the PYTHONPATH variable within a shell will only change its value for the current instance of your shell and its childen when using 'export' but is by no mean intended to change its value permanently.
Use the following command to find where to modify your path:
grep -l PYTHONPATH ~/.*
If it's hardcoded in a startup file edit its value there, spawn a new shell and voila!
Alternatively a path may be added to Python's path via a .pth file in its existing path that refers to another location.
Should this be the case erasing it permanently from Python's path should be as simple as erasing this file.