Hi @Cobion ,
Thank you for sharing your current progress.
According to the screenshot in the original description, the warning existed before the script was run.
There's a Server Manager Troubleshooting Guide on the TechNet Wiki that might help you with your refresh errors.
In addition ,I also found some similar threads ,you can try referring to the solutions in the link to see if the warning changes:
Windows Server 2012 R2 upgrade - Refresh completed with one or more warning message (microsoft.com)
Automatic Refresh Error (microsoft.com)
If none of the above suggestions help for this warning,it is recommended that you create a new thread, and add the Windows-Server related tags to get more professional help.
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