Unable to publish services from ArcGIS Pro and ArcMap after upgrading to ArcGIS Enterprise 10.9.1 (ERROR 001378)

Error Message

In certain instances, users upgrading to ArcGIS Enterprise 10.9.1 are unable to publish services from ArcGIS Pro and ArcMap. This issue affects multiple versions of ArcGIS Server, but is specific to upgrading to ArcGIS Server 10.9.1.

Note: 
If you believe that you are running into this issue, please log a case with Esri Technical Support to be added to BUG-000146553: Unable to publish services from ArcGIS Pro and ArcMap after upgrading to ArcGIS Enterprise 10.9.1 (ERROR 001378).

Cause

At ArcGIS Server 10.9.1 name and runtime changes were made for some of the ArcGIS Server system services. In some instances, these system services are not updated to use the correct runtime. In addition, some system services persist that should not be present at ArcGIS Server 10.9.1. These issues can cause publishing to fail from ArcMap and ArcGIS Pro.

Note:
The attached script has been updated. The previous script does not correct all the issues with the ArcGIS Server system services affected by the upgrade. If you ran the prior script, you may still not be able to use some enterprise workflows such as caching and analysis.
Esri advises running the latest script attached to this article.

Solution or Workaround

Download, extract, and run the script attached to this knowledge article. The script iterates through existing ArcGIS Server system services. The script deletes and re-creates system services as needed. Services that should not be present or that are using an incorrect runtime will be deleted and re-created. 

Note:
Run the script against any affected ArcGIS Server sites post upgrade. It is recommended to run the script directly from the ArcGIS Server machine. There is the potential for downtime while the system services are being re-created.

Instructions
To run the script, follow the instructions below:

1. Navigate to the ArcGIS Server python 3 directory.

Example:

C:\Program Files\ArcGIS\Server\framework\runtime\ArcGIS\bin\Python\envs\arcgispro-py3

2. Extract and run the BUG-000146553_Recreate_System_Services_updated.py script.

Example:

python.exe BUG-000146553_Recreate_System_Services_updated.py

Note: 
Provide the script name if the script is copied directly to the ArcGIS Server python directory. Alternatively, provide the file path to the script.

3. In the command prompt, provide the hostname for ArcGIS Server.

Example:

hostname.domain.com

4. When prompted, provide the username and password for an ArcGIS Server admin user.
5. Once the script is complete, review the ArcGIS Server admin directory to confirm the correct services are present.