I updated to Pro 2.2.0 today and noticed the default python environment is now read-only. The previously downloaded packages I had were wiped out with the new update. I need to get the package, spyder, back into my environment. So, I cloned the arcgispro-py3 environment in order to make the install. 
Notice that the window says, "Restart ArcGIS Pro for your environment changes to take effect."
So, I clicked 'Exit'.
After the program restarted, I no longer have a cloned environment to select.
Can someone please help?
Sounds like a pleasure ride in the country 
Hi Tim.
Since I'm in the same boat with AppData locked down for my users, and we've all been bloodied bashing our heads against the wall on this for way too long, and I've wasted too much of my own time and agencies money on something that should be so simple and a default in the software, and because I spent my entire weekend last weekend running through test environments to get things to work, let me shed some light on some unofficial workaround options.
3 easy options you have.
Option 1) Add Spyder to the default arcgispro-py3 environment via command prompt (I'd not recommend taking this route unless you are certain that you don't need to clone the default environment for anything else or if you want all your clones to have the same software installed as default (ie spyder)).
- Open Python Command Prompt as Administrator (may require you edit the the actual shortcut, or create a shortcut of your own). Dan has so graciously created a shortcut tutorial for us here: /blogs/dan_patterson/2017/07/01/arcgis-pro-2-creating-desktop-shortcuts
- Once you are up on administrative command prompt install spyder using :
conda install spyder
Option 2) Clone the default arcgispro-py3 environment to a new environment under the the original path and add Spyder to it using an administrative command prompt (safest option).
- Open Python Command Prompt as administrator same as above.
- Once you are up on administrative command prompt clone the default environment to the same root path (Pro only recognizes the Local User Directory and the Python Root path) using code similar to the following:
conda create --name "C:\Program Files\ArcGIS\Pro\bin\Python\envs\myEnvName --clone arcgispro-py3
- Activate the new environment:
- activate "C:\Program Files\ArcGIS\Pro\bin\Python\envs\myEnvName"
- Swap Project Environments in Pro:
- proswap myEnvName
- Install spyder
- conda install spyder
Option 3 (which I went with in the end and am very happy to be using)) is much trickier but much more elegant and ideal solution for the data scientist, install Anaconda Navigator and go from there:
Only attempt this if you are comfortable working with Anaconda outside of ArcGIS Pro as successfully accomplishing this (IE not screwing things up) requires understanding Anacondas installation structure and ArcGIS Pro Installs.
- Open Python Command Prompt as administrator same as above.
- Activate the root environment:
- activate root
- Install Anaconda Navigator to root. NOTE THIS WILL SCREW UP YOUR ARCGIS PRO INSTALLATION, SO YOU MUST BE READY TO FIX IT USING A REPAIR OPERATION. If you do this and you break your system that's on you. Test your workflow before moving into production.
- conda install anaconda-navigator
- Exit the Python Command Prompt and Open Windows Control Panel.
- In Windows Control Panel, Add-Remove Programs > ArcGIS Pro > Repair missing components or corrupt registry settings.
- You need to do this step because installing Anaconda Navigator changes the name of "root" env to "base" env and Pro won't work until that's repaired.
- Open Python Command Prompt as administrator same as above.
- activate root
- Open Anaconda Navigator from Command Prompt
- anaconda-navigator
- Once Anaconda Navigator opens go to Environments > arcgispro-py3 > Clone to the environment name of your choice.
- The new environment is fully accessible to Python Package Manager and ArcGIS Pro.
- Select your new environment in Navigator and add applications, update packages, or add new features to it.
Note 1 - if you require Jupyter Lab functionality best to update the ArcGIS Python package to 1.5.0 (can be done in Navigator or at the commandline using "conda install -c esri arcgis")
Note 2 - ArcGIS Pro Python Manager locks down changes to every environment under the root install directory, updating and adding packages to all environments you create using these methods requires administrative privileges and must either be done through the command line or Anaconda Navigator.
