Stephen - hmmm...that's rather odd. Whenever there's a major release like ArcGIS Pro 3.0 to 3.1, I do the update the following way to avoid "issues."
1. Complete uninstall of ArcGIS Pro 3.x
2. Rename the ESRI folder in the c:/users/<your_user_profile>/appdata/local and c:/users/<your_user_profile>/appdata/roaming to ESRI_OLD.
3. New install of ArcGIS Pro 3.1
I find this tends to avoid any weird upgrade issues. Hope this helps!