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?
Seems something is fundamentally wrong with the Conda environment. Did a clean install of Pro and experience the reported behavior from inside Pro, and even a simple create fails from cmd.
Thank you Ghislain Prince,
I almost wrote your post on Monday when running conda clean --all (as admin) fixed the issue om my computer. Then I did a bit more testing and found that clean was no silver bullet.
Of the 6 installations I have tested, 5 had the problem. Clean only fixed one of those entirely. (Allow for cloning from inside Pro) Of the other four installations, cleaning allowed creating new environments on two, but still didn't allow cloning of the arcgispro-py3 environment.
A conda list --explicit on a troubled computer shows that the arcgispro-py3 environment references some packages more than one time with different versions.
# This file may be used to create an environment using: # $ conda create --name --file # platform: win-64 @EXPLICIT https://conda.anaconda.org/esri/win-64/arcgis-1.4.1-py36h52c3b5e_1.tar.bz2 https://conda.anaconda.org/esri/win-64/arcgispro-2.2-0.tar.bz2 https://repo.continuum.io/pkgs/main/win-64/asn1crypto-0.24.0-py36_0.tar.bz2 https://repo.continuum.io/pkgs/main/win-64/atomicwrites-1.1.5-py36_0.tar.bz2 https://repo.continuum.io/pkgs/main/win-64/attrs-17.4.0-py36_0.tar.bz2 https://repo.continuum.io/pkgs/main/win-64/attrs-18.1.0-py36_0.tar.bz2 https://repo.anaconda.com/pkgs/main/win-64/backcall-0.1.0-py36_0.tar.bz2 https://repo.continuum.io/pkgs/main/win-64/bleach-2.1.3-py36_0.tar.bz2 https://repo.anaconda.com/pkgs/main/win-64/ca-certificates-2018.03.07-0.tar.bz2 https://repo.continuum.io/pkgs/main/win-64/certifi-2018.1.18-py36_0.tar.bz2 https://repo.continuum.io/pkgs/main/win-64/certifi-2018.4.16-py36_0.tar.bz2 https://repo.continuum.io/pkgs/main/win-64/cffi-1.11.5-py36h945400d_0.tar.bz2 ...
In a vanilla install of Pro 2.2 none of these duplicates occurs. Before upgrade, the Pro 2.1.3 environment on this computer looked like:
# This file may be used to create an environment using: # $ conda create --name --file # platform: win-64 @EXPLICIT https://conda.anaconda.org/esri/win-64/arcgis-1.2.5-py36_1.tar.bz2 https://conda.anaconda.org/esri/win-64/arcgispro-2.1-0.tar.bz2 https://repo.continuum.io/pkgs/main/win-64/asn1crypto-0.24.0-py36_0.tar.bz2 https://repo.continuum.io/pkgs/main/win-64/atomicwrites-1.1.5-py36_0.tar.bz2 https://repo.continuum.io/pkgs/main/win-64/attrs-18.1.0-py36_0.tar.bz2 https://repo.continuum.io/pkgs/main/win-64/backcall-0.1.0-py36_0.tar.bz2 https://repo.continuum.io/pkgs/main/win-64/bleach-2.1.3-py36_0.tar.bz2 https://repo.continuum.io/pkgs/main/win-64/ca-certificates-2018.03.07-0.tar.bz2 https://repo.continuum.io/pkgs/main/win-64/certifi-2018.4.16-py36_0.tar.bz2 https://repo.continuum.io/pkgs/main/win-64/cffi-1.11.5-py36h945400d_0.tar.bz2 ...
As you can see the Pro2.2 comes with older versions of the packages, and some packages like ca-certificates have changed repo from continuum.io to anaconda.com. After cleaning creating of new environments on this computer works fine, but cloning of the arcgispro-py3 still gives:
ERROR conda.core.link:_execute_actions(337): An error occurred while installing package 'defaults::python-3.6.5-h0c2934d_0'. CondaError: Cannot link a source that does not exist. C:\Program Files\ArcGIS\Pro\bin\Python\pkgs\python-3.6.5-h0c2934d_0\Lib\__pycache__\__future__.cpython-36.pyc Attempting to roll back. CondaError: Cannot link a source that does not exist. C:\Program Files\ArcGIS\Pro\bin\Python\pkgs\python-3.6.5-h0c2934d_0\Lib\__pycache__\__future__.cpython-36.pyc
PS: I know I should use a clone if the environment are to be used inside Pro, but it is not necessary to clone it to test for the bug. As you know, before cleaning it pops up on plain creates as well 
Hi Håkon,
thanks for reply. I noticed that late yesterday too. We've been trying to figure out a way to make conda work with this situation, we don't have it yet. We'll keep researching that.
In the meantime this works if you're willing: browse to C:\Program Files\ArcGIS\Pro\bin\Python\pkgs . Do NOT delete the cache folder, and no need to delete the *.bz2, but delete the rest of the packages folders (asn1crypto-0.24.0-py36_0, attrs-18.1.0-py36_0, backcall-0.1.0-py36_0...)
then clone & pro's python backstage worked for me.
These folders will get created from the *.bz2 files next time you need them (ie. next time you clone).
If you delete the *.bz2 files it's no big deal they'll get downloaded again (they're 80MB total).
