Alex, I have tried on my test environment and GRE is working.
Test Env:
Server1: Windows 2012R2( DP Cell manager, Backup Host, media server, disk agent, GRE agent)
Server2: VCenter6 (Pushed Advanced GRE web Plugin)
DP Version: 9.07 (I have enabled encryption directly on patch level 907. In your case you are upgrading from a previous version with encryption enabled to latest version.)
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Steps I did:
1. Checked "Configuring encrypted control communication" in GREExtensionsGuide and made sure all pre-req done.
2. Right Clicked in the DP host with GRE agent and enabled Encryption with existing certificates.
3. Took a cached backup(smarcache) and non-cached backup(file library) for a windows VM.
4. Logged in to VSphere web client and slected VM -> Manage tab
5. Selected Gear box on top right of GRE window and configured GRE Settings.
6. Did a new request and did GRE