I ve seen this a couple of times and every time i needed to redelopy the appliance.
But the culprit has always been the target storage and not VDP, i suggest you take a deepdive into you backup storage.
if you are using iSCSI take a look in the hosts vmkernel log for iSCSI deterioration entrys.
This are the things i have discorvered making VDP applainces unusable.
* Missconfigured iSCSI networks and high latency
* Port faults in FC switches and on storage arrays
* Storage controller reboots (depends on storage array) seen this with HP MSA and Whitebox solutions but never with a more fault tolerant array.
* Using deduplication on storage level