Hi,
FT-enabled VMs cannot be backed up using VADP libraries, since you need to take a snapshot of the VM in order to use VADP, but FT VMs cannot be snapshotted.
A workaround is to use a script to disable FT , run the backup and then re-enable FT. It's a trick since effectively during the backup operation the Vm is NOT protected by FT, but is the only viable method. I wrote a post about it a while ago, is based on Veeam B&R but can be applied also to other solution, if they can be scripted:
http://www.virtualtothecore.com/en/?p=3783
Luca.