Veeam Backup & Replication does not allow you to add a Fault-Tolerant (FT) VM to a backup job even if FT is temporarily disabled.
Processing of vSphere FT VMs is not supported in conjunction with vSphere 4.x or 5.x. With vSphere 6.x and Veeam Backup & Replication 8 u2, FT VMs are supported.
Please see the following article for more details: https://www.veeam.com/blog/veeam-availability-suite-update-2-vsphere-6-support-endpoint-and-more.html.
Update to both Veeam Backup & Replication 8 u2 and vSphere 6.x to enable support for FT VMs.
VMware Fault Tolerance & Snapshots: https://kb.vmware.com/selfservice/microsites/search.do?language=en_US&cmd=displayKC&externalId=1016619
VMware vSphere 6.0 Platform White Paper: http://www.vmware.com/content/dam/digitalmarketing/vmware/en/pdf/whitepaper/vsphere/vmw-white-paper-vsphr-whats-new-6-0-pltfrm.pdf