To Update the Remote App certififcate, you must do it in the Remote Desktop configuration utility. The easiest way to do this is to log into a domain controller. Open Server Manager, and add all of the remote desktop servers to the server manager application.
Once all of the servers are added you will get a Remote Desktop Management node show up on the left hand side of the window.
Clicking into that node you will see the various remote desktop options. Under tasks in the left hand side of the deployment screen you can Edit Deployment Properties.
Last option on the bottom is to manage certificates. You would be Selecting Existing. Choose a different certification path. Find the PFX and select it, enter the PFX password. Then check the last box. You may have to do this for each server in that list, clicking apply at the bottom of the deployment properties screen with each certificate change.
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