py39-six error when required by jupyter-notebook: six.cpython-39.pyc already exists and does not belong to a registered port

[afaranda]

I first received this error when I tried to install py39-jupyter, which depends on py39-six:

--->  Attempting to fetch py39-six-1.16.0_0.darwin_19.noarch.tbz2 from https://packages.macports.org/py39-six
--->  Attempting to fetch py39-six-1.16.0_0.darwin_19.noarch.tbz2.rmd160 from https://packages.macports.org/py39-six
--->  Installing py39-six @1.16.0_0
--->  Activating py39-six @1.16.0_0
Error: Failed to activate py39-six: Image error: /opt/local/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/__pycache__/six.cpython-39.pyc already exists and does not belong to a registered port.  Unable to activate port py39-six. Use 'port -f activate py39-six' to force the activation.
Error: See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_python_py-six/py39-six/main.log for details.
Error: Follow https://guide.macports.org/#project.tickets if you believe there is a bug.
Error: Processing of port py39-jupyter failed

I followed the migration instructions ​https://trac.macports.org/wiki/Migration to start with a fresh installation.

After uninstalling all of my ports and cleaning partial builds (steps c and d), I followed the instructions at ​https://trac.macports.org/wiki/ProblemHotlist#reinstall-clt to reinstall the command line tools.

After reinstalling the command line tools, I used the script restore_ports.tcl to re-install my previous ports and at first py39-six appeared to install correctly:

--->  Computing dependencies for py39-six
--->  Fetching archive for py39-six
--->  Attempting to fetch py39-six-1.16.0_0.darwin_19.noarch.tbz2 from https://packages.macports.org/py39-six
--->  Attempting to fetch py39-six-1.16.0_0.darwin_19.noarch.tbz2.rmd160 from https://packages.macports.org/py39-six
--->  Installing py39-six @1.16.0_0
--->  Cleaning py39-six

However later in the process, when py39-six activation was required as a dependency of gobject-introspection I observed a similar error as with jupyter:

--->  Activating py39-six @1.16.0_0
Error: Failed to activate py39-six: Image error: /opt/local/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/__pycache__/six.cpython-39.pyc already exists and does not belong to a registered port.  Unable to activate port py39-six. Use 'port -f activate py39-six' to force the activation.
Error: See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_python_py-six/py39-six/main.log for details.

The same problem manifested for all subsequent packages that depend on py39-six. I've attached the referenced log file, along with the "myports.txt" list of my previously installed ports that I was trying to re-install.

[afaranda]

log file referenced in the error message

[afaranda]

list of ports to re-install, generated during the migration process

[afaranda]

Listing of my terminal output during this whole process