You will need to remove the User Disk Profile mounts from the protection group. In the Core UI and on the Agent Summary page, select the volumes that are user mounts and remove them from the snapshot interval by adjusting its snapshot schedule. These volumes need to remain in a "Not Protected" state.
If there are a lot of users in the environment, this page may get cluttered. It should not affect the Core UI performance at all. As users log off the mount points will go away.
To restore from the User Disk Profiles, you will need to perform the following steps:
1) Mount the recovery point you need to restore from.
2) Within the mounted recovery point, navigate to the directory where the user's VHDx images are located. By default this would be where the UDP directory is located.
3) Right click the VHDx file and click Mount. This will mount the virtual disk in Windows File Explorer.
4) When done navigating the disk, dismount the VHDx from Disk Management and dismount the recovery point.
More information about User Profile Disk environments can be found here: http://www.virtualizationadmin.com/articles-tutorials/vdi-articles/general/working-with-user-profile-disks-on-session-based-desktop-deployments.html