It happens to the VMs that are located on the SAN. Is this normal? Are the any workarounds for this.
The first question I would ask is why are you losing SAN connectivity if you have redundant paths. If you do, and it still happens you have a major infrastructure problem. Should Windows keep cache of data forever until the drive comes back? Probably not, since that's it primary source of information retrieval and storage. There is some amount of resilience in Windows (depending on what you are doing) we have Windows VM's that go offline for hours (old hardware that fails) but as soon as I restore the connection, Windows get's rebooted (sometimes it comes back), but no corruption.
Is it ok to have all the VMs locally and have their primary storage on the SAN?
If their primary storage is on the SAN, I assume that's the drive that get's corrupted. Why do you have the storage split? You can't migrate them easily doing this. So what part of the local environment is on local disk? Have you tried to isolate why the SAN loses connectivity?
