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

Appexec links are only used briefly to find the real executable and create the access token that allows executing it. I don't know how your local profile directory ended up with a stale link. Maybe Steve has more insight.

There should be a "PythonSoftwareFoundation.Python.3.9_qbz5n2kfra8p0" subdirectory in your local "WindowsApps" directory. Check the "python3.9.exe" link in that directory as well. It's the basis for the link of the same name that gets created in the parent directory.

Note that I wrote read_appexec.py in a hurry based on someone's blog (appexec links are undocumented), which I shouldn't have trusted. I've uploaded a new version just now with what are hopefully more accurate fields and field names. The previous target path result was correct, however. For example:

    C:\>read_appexec.py "%LocalAppData%\Microsoft\WindowsApps\python3.9.exe"
    Package Name: PythonSoftwareFoundation.Python.3.9_qbz5n2kfra8p0
    Application User Model ID: PythonSoftwareFoundation.Python.3.9_qbz5n2kfra8p0!Python
    Target Path:
    C:\Program Files\WindowsApps\PythonSoftwareFoundation.Python.3.9_3.9.2288.0_x64__qbz5n2kfra8p0\python3.9.exe