Hi Justin,
I guess I didn't make it entirely clear. We have Enterprise (11.2) already setup in Azure. We migrated it from another cloud provided using the webgisdr methods and spoofed the DNS using the host files of the web adaptor, portal, and server machine. Once Enterprise was running and we had the DNS record updated to the web adaptor, everything worked fine but no external access since we initial did not route through the App Gateway. We then updated the DNS record to the App Gateway and configure the App Gateway to route to the web adaptor but it, this is when we ran into issues.
Since the App Gateway is more or less a reverse proxy would we just follow the help here,
https://enterprise.arcgis.com/en/web-adaptor/11.2/install/iis/using-a-reverse-proxy-server-with-port...
And if this is the case, "The configuration detailed in this topic must be performed before federating any ArcGIS Server site with your portal. Adding a DNS alias or reverse proxy after an ArcGIS Server site has been federated with your portal is not supported. If you need to change the host name in your organization URL, contact Esri Consulting Services or another trusted consulting partner for guidance." then the best path forward might be submitting a case. It is just unclear since when setting up we did spoof the DNS using host files when setting up and restoring to Enterprise to Azure.
