Hi, joining in on your conversation with Shaun.
> ... I've been upgraded to 3.1.0 and unfortunately the issue remains. ...
> ... No, I'm working in the default environment, ...
I'm wondering if you may have at some point installed packages into the default environment? If so, there could be problematic files left behind even after an uninstall, and these would cause problems in future installations/upgrades of Pro too.
If Shaun's suggestion to create a custom environment from scratch works, then you may want to try Clean uninstall of ArcGIS Pro - Esri BeLux to fix the corrupted installation.
> That looks like it's going to touch inaccessible directories. I'll need to engage admin.
You should normally not need to run as admin for this command, it will create the new environment in %userprofile%\esri\conda\envs. You could either ask them for write permission to that folder or for them to run the Python Command Prompt as an administrator. Otherwise, you can direct the clone to a folder where you do have write permission with the -p flag. The command would be something like this:
conda create -p C:\<your_path_to_folder_with_write_access>\pro-custom arcpy=3.1
proswap pro-custom
> What is the best management practice for admin to clone or create a new/fresh environment with all the correct packages?
Running the command from the Python Command Prompt should do the trick (arcpy=3.1 is the only package you need to specify, it will install all the required dependencies, see here).
> There were so many permission issues.
Yikes, it sounds like your machine is quite locked down. If the above fails, it'd be my main suspect and it might be helpful if your IT department calls tech support to work with a support specialist to narrow down the cause.
Shaun might have some additional thoughts, but here's the next steps I'd take:
1. Try creating the clone as per Shaun's suggestion.
2. If notebooks work in Pro with that clone active, you can either continue working with it from now on or (recommended) try Clean uninstall of ArcGIS Pro - Esri BeLux to fix the default. NOTE: Never install any packages directly into the default environment arcgispro-py3. Always clone first, then install your packages. That way, if the environment becomes corrupted, you'll always have a fallback in the default.
3. Check back with us here. Maybe there'll be new info after you try this that narrows down the problem.
4. Consider asking your IT department to work with a support specialist in tech support. You can also continue asking questions here, but a support specialist will be able to walk through the problem on your machine with the IT department and hopefully that will help resolve it.