We have been having the issue ever since applying the first update (of three) to the HPE 6.5 base image, and we ARE using the LSI Logic SAS.controller. We have been using that all along.
Also, we are running local storage - RAID1 over two 10K disks. We have moved VMs to other similar datastores to no effect. We are on the newest datastore format - VMFS 6 (and Virtual Hardware 13).
Furthermore, we have run into the exact same issue on identical hardware (HPE Proliant ML350Gen9 with local storage with Windows 2016 Server Standard VMs), so why VMware would have any difficulty recreating it is a bit of a mystery to us.
We are running thin provisioned, so the idea earlier in this thread that thick provisioned may help stills sounds viable. Hopefully others can verify.
In regards to "getting back" to the original build, if that is what some are contemplating, here are our findings (in case it may help others): It is only possible to go one "build" backwards using Shift-R. So, if you have only applied one update to your host(s), then Shift-R is still an option for you. Otherwise, as far as we can tell, the only way to get back is to boot from the original 6.5 installation media and select "Install". This operation should still retain your datastores, but may erase pretty much all other settings, such as your configuration of virtual switches (we have observed that our datastores remained, but not seen what else may be overwritten). So, at least as far as the VMs themselves go, afterwards you would just need to "add" the VMs back into your inventory (by pointing to the vmx file). However, it is always wise to MAKE A BACKUP of your VMs first (maybe just by exporting them), just in case something goes wrong.
Br,
Hans