I just wanted to provide some information to the community after experiencing some major struggles with my 10.6.1 to 10.7.1 upgrade. This is just one of the major issues faced, but the fix is easy to describe for someone who may experience the same thing. I have a base deployment on a single machine that is a reverse proxy server (deployed in our DMZ).
After upgrading to 10.7.1., my SAML authenticated logins and all of my configurable applications (Operations Dashboard, Time Aware, Compare Analysis, etc) except those built with WebApp Builder would not work. No one without built-in accounts could login to the Portal, and we could not view or create any applications from app templates.
After doing some digging, I noticed that my SAML metadata file had changed after the upgrade to point to the internal machine name URL instead of the public-facing web adaptor URL. After debugging the application websites that weren't working, I found that they had a similar problem: resources were failing to load because they were pointing to the internal URL and not the web adaptor. It was obvious that this was caused by the upgrade, but the Enterprise tech support was unable to find a solution before I did (configurable apps and SAML are not within the scope of the upgrade specialists).
I was able to talk to someone at Professional Services that provided the final fix. Though we installed and validated everything correctly during the upgrade, for some reason the internal machine name was propagated to various points within the software install instead of the public web adaptor URL.
To fix this, you need to navigate to your portaladmin page, then click system, then properties.
Update the properties by configuring and pasting the following code (note: my web adaptor is named arcgis):
Click update properties to restart the Portal, and the issue should be fixed.
Hope this helps someone! I was frantically googling and didn't find much on Geonet or Esri Resources directly related to upgrades and the machine name/web adaptor URL being swapped.