May be if you can isolate the VMs which are having issues with the error and EVC and enable the EVC on those VMs manually, you can try again post that.
check /var/log/vmware/vpxd/vpxd.log at the same time when you try to enable EVC and get error message which might provide data of VMs..
This is not tested but I am trying to isolate if there might be a VM which we can isolate causing this issue
I ran into the same issue this week with a Skylake CPU cluster (all hosts with the same 61xx CPUs, and the latest vCSA + ESXi 6.7 patches installed). I could't figure out the root cause of this, and due to time pressure we decided to evacuate some hosts, move them to a new EVC enabled cluster, and do a rolling VM power cycle to cold migrate them to the new cluster. In my case it was just a 2 node cluster with only about 20 VMs, but I can feel your pain.
IMO there's something wrong with EVC, i.e. EVC CPU features not matching the physical CPU features.Maybe worth raising a support call with VMware.