Just to reiterate there is no native change block tracking in Hyper-V on 2012R2, so Veeam uses a filter driver that gets installed on the actual Hyper-V hosts to track the changes since the previous backup. In the rare cases where there is issues with either CBT on vSphere or in your case the filter driver on Hyper-V, VBR will read each block to determine whether or not its changed since the previous backup. So in any case you're left with an incremental backup.
As stated in the link you posted above...
CBT is enabled by default. You can disable it either at the host level or at the job level for troubleshooting purposes. Note that if you choose to run incremental jobs with CBT disabled, the backup window may increase dramatically, as Veeam Backup & Replication will read all VM data to detect what blocks have changed since the last job session.
However, as Anton mentioned RCT (Resilient Change Tracking) is available in Hyper-v 2016 making the filter driver no longer required. Hope this helps.