pip 10.x adjusts where its internals are situated. The pip3 command you‘re seeing is one provided by your package maintainer (presumably debian based here?) and is not a file managed by pip.
You can read more about this on pip‘s issue tracker
You‘ll probably want to not upgrade your system pip and instead use a virtualenv.
To recover the pip3 binary you‘ll need to
sudo python3 -m pip uninstall pip && sudo apt install python3-pip --reinstall
If you want to continue in "unsupported territory" (upgrading a system package outside of the system package manager), you can probably get away with python3 -m pip ... instead of pip3.