Can someone get back to me about the 90 days disappearing, no replies to that as yet? I have had little response to questions through the case and it`s been over a month since it was initially opened so i hope you can see my frustration with communications and length of time with this.
In Update 3 we start identifying clustered VMs a bit differently (a fix to another issue). So, if you have a cluster added to backup console via SCVMM, clustered VMs (not local ones) residing on cluster nodes will get new IDs and will be treated as new ones. This will lead to new full backups and duplicated replica entities.
You had a deleted VM retention period configured. In your case the specified value was lower than selected retention period. As the result, clustered VMs with obsolete IDs that from backup server perspective were no longer processed were wiped out from backup files.