Thanks a lot for all the details.

I used the script to check all the 3.9 appexec links and only the "python3.9" one points to the wrong executable.

Version: 3
Package ID: PythonSoftwareFoundation.Python.3.9_qbz5n2kfra8p0
Entry Point: PythonSoftwareFoundation.Python.3.9_qbz5n2kfra8p0!Python
App Type: 0
Target Path:
C:\Program Files\WindowsApps\PythonSoftwareFoundation.Python.3.9_3.9.2032.0_x64__qbz5n2kfra8p0\python3.9.exe

Version: 3
Package ID: PythonSoftwareFoundation.Python.3.9_qbz5n2kfra8p0
Entry Point: PythonSoftwareFoundation.Python.3.9_qbz5n2kfra8p0!Pip
App Type: 0
Target Path:
C:\Program Files\WindowsApps\PythonSoftwareFoundation.Python.3.9_3.9.2288.0_x64__qbz5n2kfra8p0\pip3.9.exe

Could it be possible that it might not be able to replace that link when it is currently in use?

Also the "Reliability Monitor" shows a warning to install the "Python 3.9" app but I never saw anything about it in the "Windows Store".

Installation Failure: Windows failed to install the following update with error 0x80073D02: 9P7QFQMJRFP7-PythonSoftwareFoundation.Python.3.9.

A day later the success entry is found.

Installation Successful: Windows successfully installed the following update: 9P7QFQMJRFP7-PythonSoftwareFoundation.Python.3.9