I think they key problem here was that one of your functions did not use the Python session you created and thus evaluated into its own temporary session. If you use a session:

session = StartExternalSession[...]

Then all ExternalEvaluate calls should use that session:

ExternalEvaluate[session, ... ]

But some of your code used the following, which is evaluated as a one-shot evaluation:

ExternalEvaluate["Python", ... ]

Thank God! Mathematica finally has a spatial statistics function! Thank you for providing such exciting information!