I do not believe that Avamar is that smart or has that option at this time. We run Avamar against vmware and have run into leftover snapshots numerous times and it certainly isn't just due to vmotion's. As far as I can tell it is also even more a function of whether the vm can be properly quiesed for the snapshot and whether you run up against the end of your time window. We have better luck running VDR than Avamar, we just don't get the replication that Avamar offers.
Personally I think Avamar is a cumbersome beast of an application with far more complexity than is possibly needed for this service. I keep dreaming that they will bring the UI into the 21st Century.. ah to dream!