The new recovery Stick has the option to update just reinstall the hypervisor on its partition without touching the VM storage space.
To do that, you can follow the Guide: 1.4 Factory Reset and Recovery (Appliance) until you reach the Web-GUI of the recovery Stick. Choose the latest "HV-Only" Appliance OS, e.g.:
Appliance-OS-1.0.1-HV-only
And install it. It will maintain your VMs but reset the Hypervisor OS.