I think that windows executables (.venv\Scripts\*.exe) are not updated and are hardcoded to the old venv:
> py -m venv .venv
...
> .venv\scripts\Activate.ps1
...
> pip install virtualenv-clone
...
> virtualenv-clone .venv .venv2
...
> deactivate
...
> .venv2\scripts\Activate.ps1
...
> pip.exe -V
.\.venv\Lib\site-packages\pip