For your applescript solution, you could duplicate to a temporary directory (preferably on the same file system), then rename them back to the original directory. I tried to hack this together for you but gave up...
If you want an alternative, instead of bash you might look into this answer https://stackoverflow.com/a/275945/1942837 which provides a (presumably) nice python gui with progress (I have not tested this).
Okay, so apparently this was happening because tmux was holding on to the original bash version (even though I had exited tmux and reloaded it's config). tmux kill-server followed by relaunching tmux fixed it for me.
Best Answer
Yes, by putting the following line in your ~/.bash_profile file:
brewu
can be replaced by whatever alias you want to use.